2,075 research outputs found
Parallel computing and molecular dynamics of biological membranes
In this talk I discuss the general question of the portability of Molecular
Dynamics codes for diffusive systems on parallel computers of the APE family.
The intrinsic single precision arithmetics of the today available APE platforms
does not seem to affect the numerical accuracy of the simulations, while the
absence of integer addressing from CPU to individual nodes puts strong
constraints on the possible programming strategies. Liquids can be very
satisfactorily simulated using the "systolic" method. For more complex systems,
like the biological ones at which we are ultimately interested in, the "domain
decomposition" approach is best suited to beat the quadratic growth of the
inter-molecular computational time with the number of elementary components of
the system. The promising perspectives of using this strategy for extensive
simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require
A Fully Differential Digital CMOS Pulse UWB Generator
A new fully-digital CMOS pulse generator for impulse-radio Ultra-Wide-Band (UWB) systems is presented. First, the shape of the pulse which best fits the FCC regulation in the 3.1-5 GHz sub-band of the entire 3.1-10.6 GHz UWB bandwidth is derived and approximated using rectangular digital pulses. In particular, the number and width of pulses that approximate an ideal template is found through an ad-hoc optimization methodology. Then a fully differential digital CMOS circuit that synthesizes the pulse sequence is conceived and its functionality demonstrated through post-layout simulations. The results show a very good agreement with the FCC requirements and a low power consumptio
On the signature of tensile blobs in the scattering function of a stretched polymer
We present Monte Carlo data for a linear chain with excluded volume subjected
to a uniform stretching. Simulation of long chains (up to 6000 beads) at high
stretching allows us to observe the signature of tensile blobs as a crossover
in the scaling behavior of the chain scattering function for wave vectors
perpendicular to stretching. These results and corresponding ones in the
stretching direction allow us to verify for the first time Pincus prediction on
scaling inside blobs. Outside blobs, the scattering function is well described
by the Debye function for a stretched ideal chain.Comment: 4 pages, 4 figures, to appear in Physical Review Letter
Geometric Generalisations of SHAKE and RATTLE
A geometric analysis of the Shake and Rattle methods for constrained
Hamiltonian problems is carried out. The study reveals the underlying
differential geometric foundation of the two methods, and the exact relation
between them. In addition, the geometric insight naturally generalises Shake
and Rattle to allow for a strictly larger class of constrained Hamiltonian
systems than in the classical setting.
In order for Shake and Rattle to be well defined, two basic assumptions are
needed. First, a nondegeneracy assumption, which is a condition on the
Hamiltonian, i.e., on the dynamics of the system. Second, a coisotropy
assumption, which is a condition on the geometry of the constrained phase
space. Non-trivial examples of systems fulfilling, and failing to fulfill,
these assumptions are given
Integrity of H1 helix in prion protein revealed by molecular dynamic simulations to be especially vulnerable to changes in the relative orientation of H1 and its S1 flank
In the template-assistance model, normal prion protein (PrPC), the pathogenic
cause of prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine
Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to
infectious prion (PrPSc) through an autocatalytic process triggered by a
transient interaction between PrPC and PrPSc. Conventional studies suggest the
S1-H1-S2 region in PrPC to be the template of S1-S2 -sheet in PrPSc, and
the conformational conversion of PrPC into PrPSc may involve an unfolding of H1
in PrPC and its refolding into the -sheet in PrPSc. Here we conduct a
series of simulation experiments to test the idea of transient interaction of
the template-assistance model. We find that the integrity of H1 in PrPC is
vulnerable to a transient interaction that alters the native dihedral angles at
residue Asn, which connects the S1 flank to H1, but not to interactions
that alter the internal structure of the S1 flank, nor to those that alter the
relative orientation between H1 and the S2 flank.Comment: A major revision on statistical analysis method has been made. The
paper now has 23 pages, 11 figures. This work was presented at 2006 APS March
meeting session K29.0004 at Baltimore, MD, USA 3/13-17, 2006. This paper has
been accepted for pubcliation in European Biophysical Journal on Feb 2, 200
Universal behavior of localization of residue fluctuations in globular proteins
Localization properties of residue fluctuations in globular proteins are
studied theoretically by using the Gaussian network model. Participation ratio
for each residue fluctuation mode is calculated. It is found that the
relationship between participation ratio and frequency is similar for all
globular proteins, indicating a universal behavior in spite of their different
size, shape, and architecture.Comment: 4 pages, 3 figures. To appear in Phys. Rev.
Isomorphs in model molecular liquids
Isomorphs are curves in the phase diagram along which a number of static and
dynamic quantities are invariant in reduced units. A liquid has good isomorphs
if and only if it is strongly correlating, i.e., the equilibrium
virial/potential energy fluctuations are more than 90% correlated in the NVT
ensemble. This paper generalizes isomorphs to liquids composed of rigid
molecules and study the isomorphs of two systems of small rigid molecules, the
asymmetric dumbbell model and the Lewis-Wahnstrom OTP model. In particular, for
both systems we find that the isochoric heat capacity, the excess entropy, the
reduced molecular center-of-mass self part of the intermediate scattering
function, the reduced molecular center-of-mass radial distribution function to
a good approximation are invariant along an isomorph. In agreement with theory,
we also find that an instantaneous change of temperature and density from an
equilibrated state point to another isomorphic state point leads to no
relaxation. The isomorphs of the Lewis-Wahnstrom OTP model were found to be
more approximative than those of the asymmetric dumbbell model, which is
consistent with the OTP model being less strongly correlating. For both models
we find "master isomorphs", i.e., isomorphs have identical shape in the
virial/potential energy phase diagram.Comment: 20 page
Maximum Flux Transition Paths of Conformational Change
Given two metastable states A and B of a biomolecular system, the problem is
to calculate the likely paths of the transition from A to B. Such a calculation
is more informative and more manageable if done for a reduced set of collective
variables chosen so that paths cluster in collective variable space. The
computational task becomes that of computing the "center" of such a cluster. A
good way to define the center employs the concept of a committor, whose value
at a point in collective variable space is the probability that a trajectory at
that point will reach B before A. The committor "foliates" the transition
region into a set of isocommittors. The maximum flux transition path is defined
as a path that crosses each isocommittor at a point which (locally) has the
highest crossing rate of distinct reactive trajectories. (This path is
different from that of the MaxFlux method of Huo and Straub.) It is argued that
such a path is nearer to an ideal path than others that have been proposed with
the possible exception of the finite-temperature string method path. To make
the calculation tractable, three approximations are introduced, yielding a path
that is the solution of a nonsingular two-point boundary-value problem. For
such a problem, one can construct a simple and robust algorithm. One such
algorithm and its performance is discussed.Comment: 7 figure
Molecular dynamics simulation of polymer helix formation using rigid-link methods
Molecular dynamics simulations are used to study structure formation in
simple model polymer chains that are subject to excluded volume and torsional
interactions. The changing conformations exhibited by chains of different
lengths under gradual cooling are followed until each reaches a state from
which no further change is possible. The interactions are chosen so that the
true ground state is a helix, and a high proportion of simulation runs succeed
in reaching this state; the fraction that manage to form defect-free helices is
a function of both chain length and cooling rate. In order to demonstrate
behavior analogous to the formation of protein tertiary structure, additional
attractive interactions are introduced into the model, leading to the
appearance of aligned, antiparallel helix pairs. The simulations employ a
computational approach that deals directly with the internal coordinates in a
recursive manner; this representation is able to maintain constant bond lengths
and angles without the necessity of treating them as an algebraic constraint
problem supplementary to the equations of motion.Comment: 15 pages, 14 figure
Mechanical Systems with Symmetry, Variational Principles, and Integration Algorithms
This paper studies variational principles for mechanical systems with symmetry and their applications to integration algorithms. We recall some general features of how to reduce variational principles in the presence of a symmetry group along with general features of integration algorithms for mechanical systems. Then we describe some integration algorithms based directly on variational principles using a
discretization technique of Veselov. The general idea for these variational integrators is to directly discretize Hamilton’s principle rather than the equations of motion in a way that preserves the original systems invariants, notably the symplectic form and, via a discrete version of Noether’s theorem, the momentum map. The resulting mechanical integrators are second-order accurate, implicit, symplectic-momentum algorithms. We apply these integrators to the rigid body and the double spherical pendulum to show that the techniques are competitive with existing integrators
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