Exhibit F-12: Roccatano
`
` An article entitled, “Development of a Parallel Molecular Dynamics Code on SIMD Computers: Algorithm for Use of Pair List
`Criterion,” by Roccatano et al. (“Roccatano”) was published in the Journal of Computational Chemistry, vol. 19, no. 7, pp. 685-694, in
`1998 and is therefore prior art to U.S. Patent No. 7,620,800 (“’800 Patent”) at least under 35 U.S.C. §§ 102(a) and (b).
`
`As described in detail below, Roccatano anticipates the asserted claim(s) of the ’800 Patent. To the extent it is found that Roccatano
`does not expressly disclose certain limitations in the asserted claim, such limitations are inherent. Furthermore, to the extent it is
`found that Roccatano does not anticipate the asserted claim, Roccatano renders the asserted claim obvious, either alone or in
`combination with other prior art identified in the cover pleading or herein.
`
`This chart is subject to all reservations, objections, and disclaimers in Microsoft’s Invalidity Contentions and any amendment,
`supplement, or modification thereof, which are incorporated herein by reference in their entirety.
`
`
`Exemplary Disclosure of Roccatano
`
`Asserted Claim of ’800
`Patent
`[1A] A method for data
`processing in a reconfigurable
`computing system, the
`reconfigurable computing
`system comprising at least one
`reconfigurable processor, the
`reconfigurable processor
`comprising a plurality of
`functional units, said method
`comprising:
`
`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`Roccatano at Abstract: “In recent years several implementations of molecular dynamics MD codes
`have been reported on multiple instruction multiple data MIMD machines. However, very few
`implementations of MD codes on single instruction multiple data SIMD machines have been
`reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD
`codes for SIMD machines, such that, generally, the full connectivity computation has been used.
`We present an algorithm, the global cut-off algorithm GCA, which permits the use of pair lists on
`SIMD machines. GCA is based on a probabilistic approach and requires the cut-off condition to be
`simultaneously verified on all nodes of the machine. The MD code used was taken from the
`GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded
`interactions were rewritten for a parallel architecture. The remaining calculations were performed on
`the host computer. The algorithm has been tested on Quadrics computers for configurations of 32,
`128, and 512 processors and for systems of 4000, 8000, 15,000, and 30,000 particles.”
`
`Roccatano at 686: “Classical molecular dynamics MD is used to study the properties of liquids,
`solids, and molecules. The Newton equation of motion for each particle of the system is solved by
`numerical integration and its trajectory is obtained. From this microscopic point of view, many
`
`SRC Labs, LLC, et al. v. Microsoft Corp.,
`Case No. 18-cv-321 (JLR) (W.D. Wash.)
`
`1
`
`July 9, 2018
`
`

`

`Exhibit F-12: Roccatano
`
`microscopic and macroscopic properties can be obtained. The need for numerical integration limits
`the time step to the femtosecond scale and makes MD simulation a very time consuming task.
`Therefore, considerable efforts have been concentrated on optimizing MD codes on parallel
`computers of different architectures.”
`
`Roccatano at 686: “Less work has been done using SIMD systems. In general, they make use of the
`full connectivity computation; that is, all atom pair interactions are calculated, and are useful for
`long-range force systems. This is due to the difficulty of using pair lists of nonbonded atoms on
`SIMD machines with no local addressing.
`
`In the present study we propose an algorithm that permits the use of pair lists in a MD code for a
`SIMD machine with no local addressing. The algorithm requires simultaneous use of multiple time
`step and geometric decomposition methods. In addition, the systolic loop method is used to further
`reduce computation time.
`
`The method was tested on Quadrics computers, a class of SIMD machines developed by INFN and
`Alenia Spazio, for configurations of 32, 128, and 512 processors.”
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`Roccatano at 688: “GEOMETRIC DECOMPOSITION
`The assignment of the atoms to the nodes is obtained by a dynamically geometric decomposition in
`such a way that the same number of atoms is assigned to each node. In what follows, we discuss a
`decomposition for a bidimensional case; the extension to a third dimension is straightforward: given
`the bidimensional box of Figure 1a and a 2D parallel topology of n = nx x ny processors, with nx =
`
`2
`
`[1B] transforming an algorithm
`into a data driven calculation
`that is implemented by said
`reconfigurable computing
`system at the at least one
`reconfigurable processor;
`
`
`

`

`Exhibit F-12: Roccatano
`
`ny = 2, the box is first divided into nx boxes along the x-axis, as shown in Figure 1b, each
`containing the same number of atoms. Each box is successively divided into ny boxes along the y-
`axis in such a way that each one of the nx = ny boxes contains the same number of atoms (Fig. 1c).
`When, as in a real case, a third dimension exists, a successive division along the z-axis has to be
`performed.
`
`It is obvious that, before performing any division along a given axis, it is necessary to sort the
`atoms of each box along that axis. The density of a molecular system, such as a protein, is not
`uniform; thus, the boxes do not have the same axis lengths. However, these differences do not
`significantly reduce the efficiency of the GCA described in what follows.”
`
`Roccatano at Figure 1:
`
`
`
`Roccatano at 688: “Quadrics topology makes it possible to use a systolic loop to calculate the
`nonbonded interactions between the atoms assigned to the different nodes. The systolic loop method
`is one of the most efficient algorithms for calculation of two-body interactions on MIMD and SIMD
`
`
`
`3
`
`

`

`Exhibit F-12: Roccatano
`
`machines.14, 16, 24, 25 The systolic loop algorithm passes the coordinates of all atoms around a
`ring of P processors in P/2 steps, such that half of the coordinates passes every processor exactly
`once transient atoms. Each node also stores the coordinates of a group of atoms of the overall
`system resident atoms. During the systolic cycle each processor evaluates and accumulates the
`interactions of the resident atoms with the transient ones. Only half of the atoms have to pass in each
`computational node as a consequence of the reciprocity of the interactions.
`
`The systolic loop path for a 32-node Quadrics machine is shown in Figure 2. This machine has
`two nodes along the y and z directions and eight along the x direction.
`
`The geometric decomposition of the system permits limitation of the search for nonbonded
`interactions only to the neighboring processors nearer than the cut-off radius, so that, depending on
`the number of nodes and on the system size, it is generally not necessary to perform the complete
`systolic loop. The computed forces are passed back to the owning processor to accumulate the full
`force.”
`
`Roccatano at Figure 2:
`
`
`4
`
`

`

`Exhibit F-12: Roccatano
`
`Roccatano at Figure 3:
`
`
`
`
`5
`
`

`

`Exhibit F-12: Roccatano
`
`
`Roccatano at 688-89: “GLOBAL CUT-OFF ALGORITHM
`On a SIMD machine, all nodes simultaneously evaluate an interaction, but the atom pairs in each
`node are different. Figure 3 shows, as an example, the case with four nodes: suppose that each node
`is evaluating the interaction ai; in this case, all ai interactions fall within the cut-off radius. When the
`
`
`
`6
`
`

`

`Exhibit F-12: Roccatano
`
`interactions are of the bi type all the distances fall outside the cut-off radius and the interactions bi
`are skipped. In the case of interactions of type ci the interaction is outside the cut-off radius in nodes
`1, 2, and 3, but it is inside the cut-off radius in node 4, so that all nodes have to calculate this
`interaction and only will be saved in the forces calculation. If the atoms in each node are ordered
`randomly, the interactions of type ci result in being the most frequent.
`
`The basis idea of the global cut-off algorithm GCA is to maximize the occurrence of interactions of
`type ai and bi and, conversely, reduce the occurrence of interactions of type ci. To this end, it is
`necessary that the atoms in all nodes are sorted with the same criterion. Different types of sorting
`give comparable results. We have chosen the one shown in Figure 4. After this sorting procedure, a
`list of the interactions of type ai and ci is created in the integer CPU Z-CPU of the SIMD machine.
`This list is equivalent, but not identical, to the nonbonded pair list used in most MD programs and
`will be referred as the nonbonded pair list.”
`
`Roccatano at Figure 4:
`
`
`7
`
`

`

`Exhibit F-12: Roccatano
`
`
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`
`
`
`
`
`
`
`
`
`8
`
`

`

`[1C] forming at least two of
`said functional units at the at
`least one reconfigurable
`processor to perform said
`calculation
`
`[1D] wherein only functional
`units needed to solve the
`calculation are formed and
`
`[1E] wherein each formed
`functional unit at the at least
`one reconfigurable processor
`interconnects with each other
`formed functional unit at the at
`least one reconfigurable
`processor based on
`reconfigurable routing
`resources within the at least
`one reconfigurable processor
`as established at formation
`[1F] wherein lines of code of
`said calculation are formed as
`clusters of functional units
`within the at least one
`reconfigurable processor;
`
`Exhibit F-12: Roccatano
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`
`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`Roccatano at 688: “Quadrics topology makes it possible to use a systolic loop to calculate the
`nonbonded interactions between the atoms assigned to the different nodes. The systolic loop method
`is one of the most efficient algorithms for calculation of two-body interactions on MIMD and SIMD
`machines.14, 16, 24, 25 The systolic loop algorithm passes the coordinates of all atoms around a
`ring of P processors in P/2 steps, such that half of the coordinates passes every processor exactly
`once transient atoms. Each node also stores the coordinates of a group of atoms of the overall
`
`9
`
`

`

`Exhibit F-12: Roccatano
`
`system resident atoms. During the systolic cycle each processor evaluates and accumulates the
`interactions of the resident atoms with the transient ones. Only half of the atoms have to pass in each
`computational node as a consequence of the reciprocity of the interactions.
`
`The systolic loop path for a 32-node Quadrics machine is shown in Figure 2. This machine has
`two nodes along the y and z directions and eight along the x direction.
`
`The geometric decomposition of the system permits limitation of the search for nonbonded
`interactions only to the neighboring processors nearer than the cut-off radius, so that, depending on
`the number of nodes and on the system size, it is generally not necessary to perform the complete
`systolic loop. The computed forces are passed back to the owning processor to accumulate the full
`force.”
`
`Roccatano at Figure 2:
`
`
`10
`
`

`

`Exhibit F-12: Roccatano
`
`
`
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`
`11
`
`[1G] utilizing a first of said
`formed functional units to
`operate upon a subsequent data
`dimension of said calculation
`forming a first computational
`loop; and substantially
`
`

`

`concurrently utilizing a second
`of said formed functional units
`to operate upon a previous data
`dimension of said calculation
`forming a second
`computational loop
`
`Exhibit F-12: Roccatano
`
`Roccatano at 688: “Quadrics topology makes it possible to use a systolic loop to calculate the
`nonbonded interactions between the atoms assigned to the different nodes. The systolic loop method
`is one of the most efficient algorithms for calculation of two-body interactions on MIMD and SIMD
`machines.14, 16, 24, 25 The systolic loop algorithm passes the coordinates of all atoms around a
`ring of P processors in P/2 steps, such that half of the coordinates passes every processor exactly
`once transient atoms. Each node also stores the coordinates of a group of atoms of the overall
`system resident atoms. During the systolic cycle each processor evaluates and accumulates the
`interactions of the resident atoms with the transient ones. Only half of the atoms have to pass in each
`computational node as a consequence of the reciprocity of the interactions.
`
`The systolic loop path for a 32-node Quadrics machine is shown in Figure 2. This machine has
`two nodes along the y and z directions and eight along the x direction.
`
`The geometric decomposition of the system permits limitation of the search for nonbonded
`interactions only to the neighboring processors nearer than the cut-off radius, so that, depending on
`the number of nodes and on the system size, it is generally not necessary to perform the complete
`systolic loop. The computed forces are passed back to the owning processor to accumulate the full
`force.”
`
`Roccatano at Figure 2:
`
`
`12
`
`

`

`Exhibit F-12: Roccatano
`
`
`Roccatano at 689: “The basis idea of the global cut-off algorithm GCA is to maximize the
`occurrence of interactions of type ai and bi and, conversely, reduce the occurrence of interactions of
`type ci. To this end, it is necessary that the atoms in all nodes are sorted with the same criterion.
`Different types of sorting give comparable results. We have chosen the one shown in Figure 4. After
`this sorting procedure, a list of the interactions of type ai and ci is created in the integer CPU Z-CPU
`of the SIMD machine. This list is equivalent, but not identical, to the nonbonded pair list used in
`most MD programs and will be referred as the nonbonded pair list.”
`
`Roccatano at Figure 4:
`
`
`13
`
`

`

`Exhibit F-12: Roccatano
`
`
`
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`
`[1H] wherein said
`implementation of said
`calculation enables said first
`computational loop and said
`second computational loop to
`
`14
`
`

`

`execute concurrently and pass
`computed data seamlessly
`between said computational
`loops.
`
`Exhibit F-12: Roccatano
`
`Roccatano at 686: “The processors are arranged in a three-dimensional 3D cubic mesh and can
`exchange data with the six neighboring nodes, with periodic boundaries.”
`
`Roccatano at 688: “Quadrics topology makes it possible to use a systolic loop to calculate the
`nonbonded interactions between the atoms assigned to the different nodes. The systolic loop method
`is one of the most efficient algorithms for calculation of two-body interactions on MIMD and SIMD
`machines.14, 16, 24, 25 The systolic loop algorithm passes the coordinates of all atoms around a
`ring of P processors in P/2 steps, such that half of the coordinates passes every processor exactly
`once transient atoms. Each node also stores the coordinates of a group of atoms of the overall
`system resident atoms. During the systolic cycle each processor evaluates and accumulates the
`interactions of the resident atoms with the transient ones. Only half of the atoms have to pass in each
`computational node as a consequence of the reciprocity of the interactions.
`
`The systolic loop path for a 32-node Quadrics machine is shown in Figure 2. This machine has
`two nodes along the y and z directions and eight along the x direction.
`
`The geometric decomposition of the system permits limitation of the search for nonbonded
`interactions only to the neighboring processors nearer than the cut-off radius, so that, depending on
`the number of nodes and on the system size, it is generally not necessary to perform the complete
`systolic loop. The computed forces are passed back to the owning processor to accumulate the full
`force.”
`
`Roccatano at Figure 2:
`
`
`15
`
`

`

`Exhibit F-12: Roccatano
`
`
`Roccatano at 689: “The basis idea of the global cut-off algorithm GCA is to maximize the
`occurrence of interactions of type ai and bi and, conversely, reduce the occurrence of interactions of
`type ci. To this end, it is necessary that the atoms in all nodes are sorted with the same criterion.
`Different types of sorting give comparable results. We have chosen the one shown in Figure 4. After
`this sorting procedure, a list of the interactions of type ai and ci is created in the integer CPU Z-CPU
`of the SIMD machine. This list is equivalent, but not identical, to the nonbonded pair list used in
`most MD programs and will be referred as the nonbonded pair list.”
`
`Roccatano at Figure 4:
`
`
`16
`
`

`

`Exhibit F-12: Roccatano
`
`
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`17
`
`
`
`[8] The method of claim 1
`wherein said calculation
`comprises a JPEG image
`compression calculation.
`
`

`

`[9] The method of claim 1
`wherein said calculation
`comprises an MPEG image
`compression calculation.
`
`[17] The method of claim 1
`wherein said calculation
`comprises a search algorithm
`for an image search
`
`[18] The method of claim 1
`wherein said calculation
`comprises a search algorithm
`for data mining.
`
`[21] The method of claim 1
`wherein said calculation
`comprises a genetic pattern
`matching function.
`
`[22] The method of claim 1
`wherein said calculation
`comprises a protein folding
`function.
`
`Exhibit F-12: Roccatano
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`Roccatano at Abstract: “In recent years several implementations of molecular dynamics MD codes
`have been reported on multiple instruction multiple data MIMD machines. However, very few
`implementations of MD codes on single instruction multiple data SIMD machines have been
`
`18
`
`

`

`Exhibit F-12: Roccatano
`
`reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD
`codes for SIMD machines, such that, generally, the full connectivity computation has been used.
`We present an algorithm, the global cut-off algorithm GCA, which permits the use of pair lists on
`SIMD machines. GCA is based on a probabilistic approach and requires the cut-off condition to be
`simultaneously verified on all nodes of the machine. The MD code used was taken from the
`GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded
`interactions were rewritten for a parallel architecture. The remaining calculations were performed on
`the host computer. The algorithm has been tested on Quadrics computers for configurations of 32,
`128, and 512 processors and for systems of 4000, 8000, 15,000, and 30,000 particles.”
`
`Roccatano at 686: “Classical molecular dynamics MD is used to study the properties of liquids,
`solids, and molecules. The Newton equation of motion for each particle of the system is solved by
`numerical integration and its trajectory is obtained. From this microscopic point of view, many
`microscopic and macroscopic properties can be obtained. The need for numerical integration limits
`the time step to the femtosecond scale and makes MD simulation a very time consuming task.
`Therefore, considerable efforts have been concentrated on optimizing MD codes on parallel
`computers of different architectures.”
`
`Roccatano at 686: “Less work has been done using SIMD systems. In general, they make use of the
`full connectivity computation; that is, all atom pair interactions are calculated, and are useful for
`long-range force systems. This is due to the difficulty of using pair lists of nonbonded atoms on
`SIMD machines with no local addressing.
`
`In the present study we propose an algorithm that permits the use of pair lists in a MD code for a
`SIMD machine with no local addressing. The algorithm requires simultaneous use of multiple time
`step and geometric decomposition methods. In addition, the systolic loop method is used to further
`reduce computation time.
`
`The method was tested on Quadrics computers, a class of SIMD machines developed by INFN and
`Alenia Spazio, for configurations of 32, 128, and 512 processors.”
`
`Roccatano at 686: “The following molecular systems have been used as tests:
`• System 1: Box of 1536 water molecules 4608 atoms.
`
`19
`
`

`

`Exhibit F-12: Roccatano
`
`
`• System 2: Box with a BPTI (bovine pancreatic trypsin inhibitor) molecule and 2712 water
`molecules 8704 atoms.
`
`
`
`• System 3: Box with a SOD (superoxide dismutase) dimer and 4226 water molecules 15,360
`atoms.
`
`• B System 4: Box with a SOD (superoxide dismutase) dimer and 9346 water molecules
`30,720 atoms.”
`
`Roccatano at 687: “In a molecular dynamics simulation, the classical equations of motion for the
`system of interest are integrated numerically by solving Newton’s equations of motion:
`
`
`
`
`
`The solution gives the atomic positions and velocities as a function of time. The knowledge of the
`trajectory of each atom permits study of the dynamic or statistical properties of the system. The form
`of the interaction potential is complex and it includes energy terms that represent bonded and
`nonbonded van der Waals and Coulombic interactions:
`
`
`
`
`20
`
`

`

`Exhibit F-12: Roccatano
`
`
`
`
`The first four terms represent the bonded potential. b, b0, and Kb are the actual bond length, its
`reference value, and the bond stretching force constant, respectively, θ, θ0, and Kθ are the actual
`bond angle, its reference value, and the angle bending force constant, respectively, ξ, ξ0, and Kξ are
`the actual improper dihedral angle, its reference value, and the improper dihedral angle bending
`force constant, respectively. φ, Kφ, n, and δ are the actual dihedral angle, its force constant, the
`multiplicity, and the phase, respectively. The last term in the equation includes the nonbonded, van
`der Waals, and Coulombic terms. εij and σij are the dispersion well depth and the Lennard-Jones
`distance, qi and qj are the electrostatic atomic charges, rij is the distance between them, and ε is the
`dielectric constant.”
`
`
`To the extent Plaintiff asserts this limitation is not expressly or inherently disclosed under Plaintiff’s
`apparent claim construction, or any other claim construction, the claimed subject matter would have
`been obvious to a person of ordinary skill in the art considering this reference in combination with
`the knowledge of one of ordinary skill in the art at the time of the alleged invention and/or the
`disclosures in one or more of the references identified in Section I.B.2 of the cover pleading.
`
`21
`
`

`

`[23] The method of claim 1
`wherein said calculation
`comprises an organic structure
`interaction function.
`
`Exhibit F-12: Roccatano
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`At least under Plaintiff’s apparent theories of infringement and interpretations of the claims in
`alleging that any of Defendant’s accused products satisfy this claim limitation, Roccatano alone or
`in combination with one or more references, discloses:
`
`Roccatano at Abstract: “In recent years several implementations of molecular dynamics MD codes
`have been reported on multiple instruction multiple data MIMD machines. However, very few
`implementations of MD codes on single instruction multiple data SIMD machines have been
`reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD
`codes for SIMD machines, such that, generally, the full connectivity computation has been used.
`We present an algorithm, the global cut-off algorithm GCA, which permits the use of pair lists on
`SIMD machines. GCA is based on a probabilistic approach and requires the cut-off condition to be
`simultaneously verified on all nodes of the machine. The MD code used was taken from the
`GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded
`interactions were rewritten for a parallel architecture. The remaining calculations were performed on
`the host computer. The algorithm has been tested on Quadrics computers for configurations of 32,
`128, and 512 processors and for systems of 4000, 8000, 15,000, and 30,000 particles.”
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`Roccatano at 686: “Classical molecular dynamics MD is used to study the properties of liquids,
`solids, and molecules. The Newton equation of motion for each particle of the system is solved by
`numerical integration and its trajectory is obtained. From this microscopic point of view, many
`microscopic and macroscopic properties can be obtained. The need for numerical integration limits
`the time step to the femtosecond scale and makes MD simulation a very time consuming task.
`Therefore, considerable efforts have been concentrated on optimizing MD codes on parallel
`computers of different architectures.”
`
`Roccatano at 686: “Less work has been done using SIMD systems. In general, they make use of the
`full connectivity computation; that is, all atom pair interactions are calculated, and are useful for
`long-range force systems. This is due to the difficulty of using pair l