JP2005275932A - Hardware simulator - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a hardware simulator capable of resetting simulation data at high speed even in a case of a large-scaled simulation object. <P>SOLUTION: A transfer control part C13 successively stores, according to a transfer control signal instructing data transfer from a substance counter C11 to a storage device C12, a count value of the substance counter C11 to an address showing the input time of the transfer control signal of the storage device C12 during simulation. When the simulation is restarted from a certain specified point of time, the control part C13 replaces, according to a transfer control signal instructing data transfer from the storage device C12 to the substance counter C11 with an address showing the time, data of the designated address of the storage device C12 as a count value of the substance counter C11. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

  The present invention relates to a hardware simulator that is configured from predetermined hardware and that simulates the amount of change of a simulation object due to a reaction between simulation objects.

As a conventional chemical reaction simulation method, for example, by executing a simulation program on a computer, a finite temperature and a finite time are set, a molecular dynamics calculation at the finite temperature and a finite time is performed, and a molecular dynamics calculation is performed. There is a simulation apparatus that performs processing for obtaining a plurality of stable structures in which all the forces acting on all atoms of a substance are alleviated using all the structures including excited states (see Patent Document 1). At this time, in order to investigate the influence of various parameters, simulation is performed by changing various parameter values.
JP 2002-260975 A

  However, when the simulation target becomes large, when the simulation is restarted from a certain point in time or when multiple simulations are executed at the same time, in order to transfer the data at a certain point or other data as simulation data Takes a lot of time.

  An object of the present invention is to provide a hardware simulator capable of resetting simulation data at high speed even when a simulation target is large-scale.

  A hardware simulator according to the present invention is a hardware simulator that is configured of predetermined hardware and that simulates the amount of change in a simulation target due to a reaction between the simulation targets, and is provided for each simulation target. A plurality of computing elements that compute values related to the object, a reaction circuit that changes the value of the computing element according to a reaction between the simulation objects, and a value calculated by the computing element provided for each computing element A plurality of storage devices for storage.

  In the hardware simulator according to the present invention, an arithmetic element that calculates a value related to the simulation target object is provided for each simulation target object, and the value of the arithmetic element is changed according to the reaction between the simulation target objects by the reaction circuit. Thus, the amount of change of the simulation object due to the reaction between the simulation objects is simulated. At this time, since a storage device that stores the value calculated by the arithmetic element is provided for each arithmetic element, the value calculated by the arithmetic element is appropriately stored in the storage device, and stored in the storage device as necessary. The value can be set again in the arithmetic element, and the simulation data can be reset at high speed even when the simulation target is large.

  It is preferable to further include a transfer control circuit that is provided for each arithmetic element and controls the arithmetic element so as to transfer the value of the arithmetic element to the storage device. In this case, since the arithmetic element can be controlled so as to transfer the value of the arithmetic element to the storage device, the value calculated by the arithmetic element can be appropriately stored in the storage device.

  The storage device stores a plurality of values calculated by the arithmetic element, and the transfer control circuit sets the arithmetic element so as to set one value among the plurality of values stored in the storage device. It is preferable to control the storage device. In this case, since one value can be set in the arithmetic element from among a plurality of values stored in the storage device, the value stored in the storage device can be set again in the arithmetic element as necessary. Can do.

  It is preferable to further include a determination circuit that determines whether or not the value calculated by the arithmetic element is within a predetermined range. In this case, since it can be determined whether or not the value calculated by the arithmetic element is within a predetermined range, the value stored in the storage device is again stored in the arithmetic element according to the value calculated by the arithmetic element. Can be set.

  When the determination circuit determines that the value calculated by the calculation element is not within a predetermined range, the determination circuit sets one value among the plurality of values stored in the storage device to the calculation element. It is preferable to control the transfer control circuit.

  In this case, when it is determined that the value calculated by the calculation element is not within the predetermined range, one value can be set in the calculation element from among a plurality of values stored in the storage device. When the value calculated by the element becomes an unnecessary value as a simulation result, the simulation can be continued again using an appropriate value.

  A first determination circuit that determines whether or not a value calculated by a predetermined calculation element among the plurality of calculation elements satisfies a predetermined condition; and when the first determination circuit determines that the predetermined condition is satisfied It is preferable that the apparatus further includes a second determination circuit that determines whether or not a value based on a value calculated by a predetermined calculation element among the plurality of calculation elements is within a predetermined range.

  In this case, it is determined whether or not a value calculated by a predetermined calculation element among a plurality of calculation elements satisfies a predetermined condition, and when such a condition occurs, a value based on the value calculated by the calculation element is determined. Since it can be determined whether or not it is within a predetermined range, the computing element calculates while considering complex conditions such as when a certain substance reacts on the condition that a certain substance satisfies a predetermined condition. The value stored in the storage device can be set again in the arithmetic element in accordance with the value based on the obtained value.

  When the second determination circuit determines that a value based on a value calculated by the predetermined calculation element is not within a predetermined range, the second determination circuit stores a plurality of storage devices provided for the calculation element. It is preferable to control the transfer control circuit so that one of the values is set in the arithmetic element.

  In this case, when it is determined that the value based on the value calculated by the calculation element is not within the predetermined range, one value can be set as the calculation element from among a plurality of values stored in the storage device. Therefore, the simulation can be continued again using an appropriate value when the value calculated by the calculation element becomes an unnecessary value as a simulation result while considering the above complicated condition.

  According to the present invention, when the amount of change of the simulation object due to the reaction between the simulation objects is simulated, the storage device that stores the value calculated by the calculation element is provided for each calculation element. The value calculated by the element can be stored in the storage device as needed, and the value stored in the storage device can be set again in the storage element as necessary. Even when the simulation target is large, simulation data can be stored at high speed. Can be reset.

  Hereinafter, as an example of a hardware simulator according to the present invention, a chemical reaction simulation apparatus that simulates a biochemical reaction and is suitably used for elucidating a signal transmission network, a gene network, and the like will be described with reference to the drawings.

  FIG. 1 is a block diagram showing a configuration of a hardware simulator according to the first embodiment of the present invention. The hardware simulator shown in FIG. 1 includes a plurality of random number generators R1 to Rn (n is an arbitrary positive number), a plurality of enzyme counters K1 to Kn, a plurality of throttle circuits V1 to Vn, and a plurality of reaction execution circuits H1 to Hn. And a plurality of counter units C1 to Cm (m is an arbitrary positive number) and a connection switching circuit SW. The enzyme counters K1 to Kn, the diaphragm circuits V1 to Vn, and the reaction execution circuits H1 to Hn are provided for each biochemical reaction used for the simulation, and the counter units C1 to Cm are provided for each substance used for the simulation. .

  The random number generator R1 is connected to the input side of the aperture circuit V1, the reaction execution circuit H1 is connected to the output side of the aperture circuit V1, and the enzyme counter K1 is connected to the aperture circuit V1. Other random number generators, enzyme counters, throttle circuits, and reaction execution circuits are also connected in the same manner as described above.

  The connection switching circuit SW is composed of, for example, a space switch or the like, and includes a plurality of increase command input wires I1 to In and a decrease command input wires D1 to Dn, and a plurality of increase command output wires i1 to im. The output wirings d1 to dm for reduction command are included, and each wiring is arranged in a matrix. The reaction execution circuit H1 is connected to the input wiring I1 for increase command and the input wiring D1 for decrease command of the connection switching circuit SW, and other reaction execution circuits are similarly connected.

  FIG. 2 is a block diagram showing an example of the configuration of the counter unit C1 shown in FIG. The counter unit C1 illustrated in FIG. 2 includes a substance counter C11, a storage device C12, and a transfer control unit C13. The other counter units C2 to Cm are similarly configured and operate in the same manner as described below.

  The substance counter C11 is composed of, for example, a binary counter or the like, and is connected to the output wiring i1 for increase command and the output wiring d1 for decrease command of the connection switching circuit SW. In the substance counter C11, the number of each substance before the reaction, that is, the number of molecules or the number of atoms is set as an initial count value, and the count value is decreased and increased according to the decrease command and the increase command of the reaction execution circuits H1 to Hn. Let The substance counter is not particularly limited to the binary counter described above, and any other counter or the like may be used as long as it is an arithmetic element that is provided for each simulation target and calculates a value related to the simulation target. For example, when a biochemical reaction such as a citric acid circuit in a metabolic pathway is regarded as a state transition and used in combination with a state transition machine (finite state automaton), a Johnson counter is used as a substance counter, thereby enabling a faster and more compact circuit. Can be simulated.

  The transfer control unit C13 controls data transfer from the substance counter C11 to the storage device C12 and data transfer from the storage device C12 to the substance counter C11 according to a transfer control signal input from the outside. Specifically, when receiving a transfer control signal instructing data transfer from the substance counter C11 to the storage device C12, the transfer control unit C13 stores the count value of the substance counter C11 at a predetermined address in the storage device C12. . When the transfer control unit C13 receives a transfer control signal instructing data transfer from the storage device C12 to the substance counter C11, the transfer control unit C13 replaces the data at the designated address in the storage device C12 as the count value of the substance counter C11. For example, when instructed to transfer the data D1 at the address A1 from the storage device C12 to the substance counter C11, the transfer control unit C13 transfers the data D1 at the address A1 to the substance counter C11 with respect to the storage device C12. The storage device C12 transfers the data D1 at the address A1 to the substance counter C11.

  The storage device C12 is not particularly limited to the one that operates according to the above addressing, and various storage devices can be used. A stack type storage device (LIFO) or the like from which the last transferred data is first extracted is used. May be used. Further, when an address is used with the address portion as a simulation time, it is preferable to use an associative memory (Content Addressable Memory). In this case, the addressing of the storage device designates the contents of the address part, and the desired data can be transferred efficiently.

  Referring again to FIG. 1, in the connection switching circuit SW, a switch composed of a time-division gate and a holding memory for controlling on / off of the time-division gate at the intersection ND of each wiring indicated by a black circle in the figure (Not shown) is arranged. The connection switching circuit SW turns on / off each switch to connect the increase command input wirings I1 to In to the plurality of increase command output wires i1 to im and decrease command input wirings D1 to D1. A substance counter that represents a substance before the reaction of a biochemical reaction represented by each reaction execution circuit H1 to Hn, and a substance counter that represents a substance after the reaction, which controls the connection state between Dn and the output wirings d1 to dm for decrease command Connect the corresponding reaction execution circuit. The connection switching circuit SW is not particularly limited to the above space switch, and other connection switching circuits may be used as long as the connection state between the reaction execution circuit and the substance counter can be switched.

  The random number generator R1 outputs a predetermined random number for controlling the reaction rate of the biochemical reaction to the reaction execution circuit H1 via the throttle circuit V1. As the random number generator, a pseudo random number generation circuit that generates pseudo random numbers, a chaos generation circuit that generates chaotic random numbers, a thermal noise generation circuit that generates random numbers based on thermal noise, and the like can be used.

For example, as a pseudo-random number generation circuit, a linear feedback shift register is used, and when the linear feedback shift register is composed of L registers, a random number having a long period of 2 ^L -1 is generated. Can be made. As the chaos generation circuit, an irregular random number that performs chaotic behavior can be generated by using a circuit that generates an irregular signal by a closed loop including a capacitor and a variable resistance circuit. As a thermal noise generation circuit, by using a circuit that latches short cycle pulses with long cycle pulses and outputs the level of the latched short cycle pulses as random numbers, random numbers without periodicity due to white noise can be generated. Can be generated.

  The enzyme counter K1 is set with the number of enzyme substances used in the biochemical reaction represented by the reaction execution circuit H1, that is, the number of molecules of the enzyme substance as its count value, and the aperture of the aperture circuit V1 according to the set count value. The amount is adjusted. In the case of a general chemical reaction, the enzyme counter is changed to a catalyst counter, and the number of catalytic substances is set as the count value instead of an enzyme that is a protein biocatalyst produced in living cells. In the case of a chemical reaction that does not use a catalyst (enzyme), a catalyst (enzyme) counter and a throttle circuit are not required.

  Specifically, the random number generator R1 randomly generates “1” or “0” data as a random number, and the enzyme counter K1 adjusts the frequency of “1” with respect to “0” according to the count value. Data of “1” or “0” is output. At this time, the aperture circuit V1 takes the logical product of both data and outputs the result to the reaction execution circuit H1. Therefore, the frequency of “1” input to the reaction execution circuit H1 is adjusted according to the count value of the enzyme counter K1.

  When “1” is input as data, the reaction execution circuit H1 outputs an increase command for increasing the count value by 1 to the increase command input wiring I1 and executes a decrease command. A decrease command for decreasing the count value by 1 is output to the input wiring D1. On the other hand, when “0” is input as data, the reaction execution circuit H1 does not output an increase command and a decrease command so as not to perform a reaction (non-execution state).

  At this time, the connection switching circuit SW is connected to the input wiring D1 for decrease command and the substance counter representing the number of substances before reaction in the biochemical reaction represented by the reaction execution circuit H1, that is, the number of molecules or the number of atoms. The output wiring for the reduction command is connected. Therefore, the decrease command output from the reaction execution circuit H1 is input to the substance counter provided for the substance before the reaction, and the substance counter decreases its count value by one. The connection switching circuit SW is connected to an increase command input wiring I1 and a substance counter representing the number of substances after reaction in the biochemical reaction represented by the reaction execution circuit H1, that is, the number of molecules or the number of atoms. The output wiring for command is connected. Therefore, the increase command output from the reaction execution circuit H1 is input to the substance counter provided for the substance after the reaction, and the substance counter increases its count value by one.

  Other random number generators, enzyme counters, throttling circuits, and reaction execution circuits are also configured in the same manner as described above, and operate in the same manner as described above according to biochemical reactions. When the number of enzymes assigned to the enzyme counter increases or decreases due to a biochemical reaction or the like, the enzyme counter is also configured in the same way as the substance counter and is connected to the connection switching circuit, and the count value is increased or decreased by the corresponding reaction execution circuit. Is done.

  In the present embodiment, the substance counter C11 corresponds to an example of an arithmetic element, and the reaction execution circuits H1 to Hn, the random number generators R1 to Rn, the enzyme counters K1 to Kn, the throttling circuits V1 to Vn, and the connection switching circuit SW are reacted. The storage device C12 corresponds to an example of a circuit, the storage device C12 corresponds to an example of a storage device, and the transfer control unit C13 corresponds to an example of a transfer control circuit.

  Next, the operation of the hardware simulator configured as described above will be described. First, using the necessary data regarding the substance to be simulated, biochemical reaction, enzyme, and the like, the initial value of the counter indicating the number of each substance is set in the substance counter C11 of each counter unit C1 to Cm, The initial value of the counter indicating the number of each enzyme is set in the enzyme counters K1 to Kn. Next, the random number generators R1 to Rn generate the above random numbers, and the diaphragm circuits V1 to Vn correct the random numbers according to the number of enzymes in the enzyme counters K1 to Kn. The reaction execution circuits H1 to Hn decrease the count value of the substance counter C11 indicating the number of molecules or atoms of the substance before the reaction by 1 so that the reaction is executed according to the random number value corrected by the number of enzymes. At the same time, the count value of the substance counter C11 indicating the number of molecules or atoms of the substance after the reaction is increased by one.

  In this way, the reaction rate of the biochemical reaction represented by each reaction execution circuit H1 to Hn is adjusted for each reaction execution circuit H1 to Hn, and the substances before and after the reaction of the biochemical reaction represented by each reaction execution circuit H1 to Hn are adjusted. The corresponding substance counter C11 is connected to the corresponding reaction execution circuit H1 to Hn, and the count value of the substance counter C11 corresponding to the substance before and after the reaction is decreased according to the biochemical reaction represented by each reaction execution circuit H1 to Hn. Or increased and multiple biochemical reactions are simulated in parallel.

  In this way, the amount of each substance before and after the reaction is regarded as a count value, that is, a number (integer), and the amount of change in the substance due to the biochemical reaction is simulated. The types of substances used can be increased. In addition, even when an unknown biochemical reaction is newly found, a new biochemical reaction or deficiency is detected even if a biochemical reaction is deficient due to a disease etc. It can be easily dealt with by changing the connection state between the reaction execution circuits H1 to Hn and the substance counter C11 of the counter units C1 to Cm by the connection switching circuit SW according to the biochemical reaction performed and the biochemical reaction different from the normal one. Can do.

  Further, during the above simulation, a transfer control signal instructing data transfer from the substance counter C11 to the storage device C12 is sequentially input from the outside at a predetermined timing together with an address indicating time, and transfer control of each counter unit C1 to Cm is performed. The unit C13 sequentially stores the count value of the substance counter C11 at an address indicating the time when the transfer control signal of the storage device C12 is input. Thereafter, when the simulation operation is stopped and the simulation is restarted from a specific time point, a transfer control signal for instructing data transfer from the storage device C12 to the substance counter C11 is input to the counter units C1 to Cm together with an address indicating the time. Then, the transfer control unit C13 of each counter unit replaces the data at the designated address in the storage device C12 as the count value of the substance counter C11.

  As described above, since the storage device C12 that stores the count value of the material counter C11 of the counter units C1 to Cm is provided for each material counter C11, the count value of the material counter C11 is appropriately stored in the storage device C12. Accordingly, the count value stored in the storage device C12 can be set again in the substance counter C11, and simulation data can be set at high speed even when the simulation target is large.

  In the present embodiment, the count value of the substance counter C11 is stored in the storage device C12 in all the counter units C1 to Cm. However, the present invention is not particularly limited to this example, and the count value is only in a part of the counter units. May be stored, or only one predetermined value may be stored without storing a plurality of count values stored in the storage device C12.

  FIG. 3 is a block diagram showing a configuration of another counter unit C1a that can be used as the counter units C1 to Cm shown in FIG. The difference between the counter unit C1a shown in FIG. 3 and the counter unit C1 shown in FIG. 2 is that a data value range holding device C14 and a comparator C15 are added, and the transfer control unit is in accordance with the transfer control signal output by the comparator C15. The other points are the same as those of the counter unit C1 shown in FIG.

  The data value range holding device C14 includes a predetermined memory or a register, and stores the maximum value and the minimum value in advance as the data value range of the substance counter C11. The comparator C15 compares the maximum value and the minimum value held by the data value range holding device C14 with the count value of the substance counter C11, and compares the maximum value and the minimum value held by the data value range holding device C14. It is determined whether or not the count value of the substance counter C11 is entered during the period. For example, when a chemical reaction simulation is performed to try to reproduce a certain phenomenon, the amount of the substance that each substance counter C11 is simulating in the target phenomenon is known. By setting as, efficient simulation can be performed. Further, when the relationship between a certain substance and another substance is known to some extent, the relation with the count value of the substance counter C11 that simulates another substance can be described.

  Here, when there is no count value between the maximum value and the minimum value, the comparator C15 substitutes a predetermined count value among the plurality of count values stored in the storage device C12 for the substance counter C11. A transfer control signal instructing to do so is output to the transfer control unit C13a. The transfer control unit C13a replaces the count value of the designated storage device C12 as the count value of the substance counter C11. In this example, the transfer control unit C13a corresponds to an example of a transfer control circuit, and the data value range holding device C14 and the comparator C15 correspond to an example of a determination circuit.

  For example, at an arbitrary time T1, the count value of the substance counter C11 is stored in the storage device C12, and then the simulation is executed using the plurality of parameter sets 1 to N until the time T2. Next, when the amount of the specific chemical substance is not within the assumed data value range in the simulation using the parameter set other than the parameter set 3 at time T2, the parameter set other than the parameter set 3 is incorrect. I understand that. Therefore, the count value stored in the storage device C12 at the time T1 can be set in the substance counter C11, and the simulation from the time T1 can be resumed using another parameter set. Thus, instead of executing the simulation to the end, it is possible to efficiently execute the simulation while narrowing down the parameter values used for the simulation, and the simulation time can be greatly shortened.

FIG. 4 is a schematic diagram for explaining an example of simulation by the hardware simulator shown in FIG. The example shown in FIG. 4 shows Glycolysis (glycolysis) which is a metabolic process for degrading glucose (glucose). Hexokinase (hexokinase) becomes an enzyme, and glucose 6P (glucose-P) is converted from glucose and ATP (adenosine triphosphate). 6-phosphate), ADP (adenosine diphosphate) and H ₊ are produced.

  In this example, first, a predetermined random number is input from the random number generator R to the aperture circuit V. At this time, the number of hexokinase molecules is set as the count value in the enzyme counter K, the output of the squeezing circuit V is squeezed according to the number of hexokinase molecules, and according to the random number of the random number generator R and the number of hexokinase molecules. Thus, execution and non-execution of Glycolysis by the reaction execution circuit H are controlled.

The reaction execution circuit H includes substance counters C11a and C11b that represent the number of molecules of glucose and ATP that are substances before the reaction, and a substance counter C11c that represents the number of molecules or atoms of glucose 6P, ADP, and H ₊ that are substances after the reaction. , C11d, and C11e are connected by a connection switching circuit (not shown).

  The reaction execution circuit H instructs the substance counters C11a and C11b to decrease the count value by 1 when the data output through the aperture circuit V is “1”, that is, when the reaction is executed. C11c, C11d, and C11e are instructed to increase the count value by 1, the material counters C11a and C11b decrease the count value by 1, and the material counters C11c, C11d, and C11e increase the count value by 1. .

In this manner, using the hardware simulator shown in FIG. 1, the amount of change of each substance due to Glycolysis that generates glucose 6P, ADP, and H ₊ from glucose and ATP can be simulated using hexokinase as an enzyme.

  At this time, at time T1, a transfer control signal instructing data transfer from each of the substance counters C11a to C11e to each of the storage devices C12a to C12e is input from the outside to a transfer control unit (not shown), and each of the substance counters C11a to C11e Count values A to E are stored in the storage devices C12a to C12e. Thereafter, when the simulation is restarted from time T1, a transfer control signal instructing data transfer from each of the storage devices C12a to C12e to each of the substance counters C11a to C11e is input to the transfer control unit and stored in each of the storage devices C12a to C12e. The counted values A to E are set in the substance counters C11a to C11e, and the simulation can be restarted from time T1.

  Next, a case where a biochemical reaction in a cell is simulated in consideration of a concentration gradient of each substance in the cell will be described. FIG. 5 is a schematic diagram for explaining a method of simulating a biochemical reaction in a cell in consideration of a concentration gradient of each substance in the cell.

  As shown in FIG. 5, when simulating a biochemical reaction in a cell, one cell is divided into a plurality of cells CE, the amount of the substance is held for each cell CE, and the concentration gradient of each substance is obtained by a cellular automaton. To simulate. That is, the diffusion of each substance between cells is simulated from the concentration (amount) of each substance in the target cell and the concentrations (amounts) of substances in the six neighboring cells.

  For example, when two adjacent cells C1 and C2 contain substances 1, 2 and 3 having different concentrations, each substance diffuses from the higher concentration to the lower cell C1 and C2. The diffusion between the cells can be simulated as follows.

  FIG. 6 is a block diagram showing a configuration of a hardware simulator in the case of simulating the diffusion of substances in the two cells shown in FIG. The hardware simulator shown in FIG. 6 includes a hardware simulator CB1 for the cell C1, a hardware simulator CB2 for the cell C2, and a diffusion circuit KC.

  Each count value of the substance counters C111 to C113 in the hardware simulator CB1 shown in FIG. 6 represents the number of molecules or atoms of the substances 1 to 3 in the cell C1, and the substance counters C111 ′ to C111 ′ in the hardware simulator CB2 Each count value of C113 ′ represents the number of molecules or atoms of the substances 1 to 3 in the cell C2, and the substance counters C111 to C113 and C111 ′ to C113 ′ are connected via the diffusion circuit KC. .

  The diffusion circuit KC includes substance counters C111 to C113 and C111 ′ to C113 so that each substance diffuses according to the count values of the substance counters C111 to C113 and C111 ′ to C113 ′, that is, the number of molecules or atoms of each substance. Control the count value of '. For example, when the count value of the substance counter C111 is larger than the count value of the substance counter C111 ′, the count value of the substance counter C111 is sequentially decreased according to a predetermined diffusion rate until the equilibrium state is reached, and the substance is made corresponding to this. The count value of the counter C111 ′ is sequentially increased.

  In FIG. 6, only the material counters C111 to C113, C111 ′ to C113 ′ and the storage devices C121 to C123 and C121 ′ to C123 ′ are illustrated in the hardware simulators CB1 and CB2 for the cells C1 and C2. The hardware simulators CB1 and CB2 are also configured in the same manner as the hardware simulator shown in FIG. 1, and have a random number generator, an enzyme counter, a throttling circuit, a reaction execution circuit, a connection switching circuit, and a transfer control unit (not shown). ing. Therefore, the hardware simulators CB1 and CB2 also operate in the same manner as the hardware simulator shown in FIG. 1, the internal biochemical reaction is simulated for each of the cells C1 and C2, and the material counters C111 to C111 are controlled according to the transfer control signal. The count values of C113, C111 ′ to C113 ′ are stored in the storage devices C121 to C123 and C121 ′ to C123 ′, and the count values stored in the storage devices C121 to C123 and C121 ′ to C123 ′ are the substance counter C111. To C113 and C111 ′ to C113 ′.

  As described above, the cell is divided into a plurality of cells, and the amount of change of the substance due to the biochemical reaction is simulated for each cell, and each substance in the cell is simulated by simulating the diffusion of each substance between adjacent cells. The amount of change of the substance in the cell can be simulated in consideration of the concentration gradient of the substance, and the count value of the substance counter is appropriately stored in the storage device, and the count value stored in the storage device is stored as necessary. The substance counter can be set again.

  Next, a case where a multicellular biochemical reaction is simulated will be described. FIG. 7 is a schematic diagram for explaining a method of simulating a multicellular biochemical reaction. As shown in FIG. 7, each cell is divided into a plurality of cells CE (cells without hatching in the figure) as in FIG. 5, and the cell wall existing between the cells is divided into a plurality of cell wall cells WC (hatching in the figure). Cell). In this case, in each cell, a biochemical reaction is simulated in the same manner as the intracellular simulation described with reference to FIGS.

  In addition, the portion of the cell wall cell WC that represents the cell wall may be simulated, for example, as diffusion does not occur, that is, the substance does not diffuse between cells. Similar to the cell cell, diffusion may be simulated using a diffusion circuit.

  As described above, each cell is divided into a plurality of cells, the cell wall is divided into a plurality of cell wall cells, the amount of change of the substance due to the biochemical reaction is simulated for each cell, and between adjacent cells in the cell By simulating the diffusion of each substance, the biochemical reaction of multicells is similarly simulated, and the count value of the substance counter is appropriately stored in the storage device, and stored in the storage device as necessary. The count value can be set again in the substance counter.

  Next, a hardware simulator according to the second embodiment of the present invention will be described. FIG. 8 is a block diagram showing a configuration of a hardware simulator according to the second embodiment of the present invention. The difference between the hardware simulator shown in FIG. 8 and the hardware simulator shown in FIG. 1 is that a data value range holding device DH, a comparator CM, a calculation device CD, and a reaction condition detection network circuit SN are added. Since the other points are the same as those of the hardware simulator shown in FIG. The counter units C1 to Cm are configured similarly to the counter unit shown in FIG.

  The counter units C2 to Cm output the count value of their own substance counter C11 (see FIG. 2) to the network circuit SN. The reaction condition detection network circuit SN is composed of a predetermined logic circuit or the like, and counts the count values of the counter units C2 to Cm to determine whether or not the predetermined reaction condition is satisfied, thereby satisfying the reaction condition. If it is determined, the reaction enable signal is output to the arithmetic unit CD. As the reaction condition detection network circuit SN, for example, a small world network having both the characteristics of a random network with a short average path length and the characteristics of a regular network with a large cluster coefficient can be used. There is no limitation, and other networks may be used.

  The counter unit C1 outputs the count value of its own substance counter C11 to the arithmetic device CD. When receiving a reaction enable signal from the reaction condition detection network circuit SN, the arithmetic device CD performs a predetermined calculation on the count value of the counter unit C1, and outputs the calculated value calculated from the count value to the comparator CM. . When the count value of the substance counter C11 is used as it is, the arithmetic device CD outputs the count value of the substance counter C11 as it is to the comparator CM. In this case, the data value range holding device DH stores the data value range of the count value of the counter unit C1.

  The data value range holding device DH stores the maximum value and the minimum value in advance as a data value range of values calculated from the count value of the counter unit C1. The comparator CM compares the maximum value and the minimum value held by the data value range holding device DH with the calculated value of the calculation device CD, and determines the maximum value and the minimum value held by the data value range holding device DH. It is determined whether or not the operation value of the operation device CD is included in between. The comparator CM has a predetermined count value out of a plurality of count values stored in the storage device C12 (see FIG. 2) of the counter unit C1 when there is no calculated value between the maximum value and the minimum value. Is transferred to the transfer control unit C13 (see FIG. 2). The transfer control unit C13 replaces the designated count value of the storage device C12 as the count value of the substance counter C11. In the present embodiment, the reaction condition detection network circuit SN corresponds to an example of a first determination circuit, and the arithmetic device CD, the data value range holding device DH, and the comparator CM correspond to an example of a second determination circuit.

  As described above, in the present embodiment, it is determined whether or not the substance amounts of the counter units C2 to Cm satisfy a predetermined reaction condition, and a value calculated from the count value of the counter unit C1 when the reaction condition is satisfied. Is determined to be within the assumed data value range, and when the value is not within the data value range, the count value before the predetermined time stored in the storage device C12 is set in the substance counter C11. The value calculated from the count value of the counter unit C1 is within an assumed data value range while taking into account complicated conditions such as when a certain substance reacts on condition that a plurality of substances satisfy a predetermined condition. When the count value of the substance counter C11 becomes an unnecessary value as a simulation result, the simulation can be restarted by setting an appropriate count value again. Kill.

  In the present embodiment, it is determined whether or not the reaction condition is satisfied from the count values of the counter units C2 to Cm. However, the present embodiment is not particularly limited to this example, and even if it is determined from the count values of other counter units. Also, the counter unit in which the count value is set is not particularly limited to the counter unit C1, and the count value of another counter unit may be set.

  The hardware simulator to which the present invention is applicable is not particularly limited to the above example, and is a hardware simulator that is configured from predetermined hardware and that simulates the amount of change in the simulation target due to the reaction between the simulation targets. If it exists, it is applicable to various fields. For example, biological simulation of brain cells and neural networks, genetic evolution and individual evolution simulation of living organisms, ecosystem simulation for migratory bird movement, transportation system simulation for moving objects, evacuation simulation, numerical fluid simulation, weather simulation, logistics simulation , Power supply simulation, city simulation for city planning, etc., economic system simulation for business transactions and stock / future transactions, management simulation, electromagnetic simulation of electrical circuits and integrated circuits, electronic level simulation of semiconductors and materials Can do.

It is a block diagram which shows the structure of the hardware simulator by the 1st Embodiment of this invention. It is a block diagram which shows the structure of an example of the counter part shown in FIG. It is a block diagram which shows the structure of the other counter part which can be used as a counter part shown in FIG. It is a schematic diagram for demonstrating the example of the simulation by the hardware simulator shown in FIG. It is a schematic diagram for demonstrating the method of simulating the biochemical reaction in a cell in consideration of the concentration gradient of each substance in a cell. It is a block diagram which shows the structure of the hardware simulator in the case of simulating the spreading | diffusion of the substance in two cells shown in FIG. It is the schematic for demonstrating the method of simulating the biochemical reaction of a multicell. It is a block diagram which shows the structure of the hardware simulator by the 2nd Embodiment of this invention.

Explanation of symbols

R1-Rn Random number generator K1-Kn Enzyme counter V1-Vn Aperture circuit H1-Hn Reaction execution circuit SW Connection switching circuit C1-Cm, C1a Counter unit C11 Substance counter C12 Storage device C13, C13a Transfer control unit C14, DH Data value Range holding device C15, CM comparator CD arithmetic unit SN reaction condition detection network circuit

Claims (7)

A hardware simulator configured with predetermined hardware and simulating the amount of change of a simulation object due to a reaction between simulation objects,
A plurality of computing elements that are provided for each simulation target and calculate values related to the simulation target;
A reaction circuit that changes a value of an arithmetic element according to a reaction between the simulation objects;
A hardware simulator comprising a plurality of storage devices that are provided for each of the arithmetic elements and store values calculated by the arithmetic elements.   The hardware simulator according to claim 1, further comprising a transfer control circuit that is provided for each arithmetic element and controls the arithmetic element so as to transfer the value of the arithmetic element to the storage device. The storage device stores a plurality of values calculated by the calculation element,
3. The hardware according to claim 2, wherein the transfer control circuit controls the storage device so as to set one value among the plurality of values stored in the storage device in the arithmetic element. Simulator.   4. The hardware simulator according to claim 3, further comprising a determination circuit that determines whether or not a value calculated by the arithmetic element is within a predetermined range.   When the determination circuit determines that the value calculated by the calculation element is not within a predetermined range, the determination circuit sets one value among the plurality of values stored in the storage device to the calculation element. 5. The hardware simulator according to claim 4, wherein the transfer control circuit is controlled. A first determination circuit that determines whether or not a value calculated by a predetermined calculation element among the plurality of calculation elements satisfies a predetermined condition;
When the first determination circuit determines that a predetermined condition is satisfied, the first determination circuit determines whether a value based on a value calculated by a predetermined calculation element among the plurality of calculation elements is within a predetermined range. 4. The hardware simulator according to claim 3, further comprising: 2 determination circuits.   When the second determination circuit determines that a value based on a value calculated by the predetermined calculation element is not within a predetermined range, the second determination circuit stores a plurality of storage devices provided for the calculation element. 7. The hardware simulator according to claim 6, wherein the transfer control circuit is controlled so as to set one value among the values to the arithmetic element.

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