421 research outputs found
Multiphoton Absorption of Myoglobin–Nitric Oxide Complex: Relaxation by D-NEMD of a Stationary State
ABSTRACT:
The photodissociation and geminate recombination of nitric oxide in
myoglobin, under continuous illumination, is modeled computationally. The
relaxation of the photon energy into the protein matrix is also considered in a
single simulation scheme that mimics a complete experimental setup. The dynamic
approach to non-equilibrium molecular dynamics is used, starting from a steady
state, to compute its relaxation to equilibrium. Simulations are conducted for the
native form of sperm whale myoglobin and for two other mutants, V68W and L29F,
illustrating a fair diversity of spatial and temporal geminate recombination processes.
Energy flow to the heme and immediate protein environment provide hints to
allostery. In particular, a pathway of energy flow between the heme and the FG loop
is illustrated. Although the simulations were conducted for myoglobin only, the thermal fluctuations of the FG corner are in
agreement with the large structural shifts of FG during the allosteric transition of tetrameric hemoglobin
Accessibility for Line-Cutting in Freeform Surfaces
Manufacturing techniques such as hot-wire cutting, wire-EDM, wire-saw cutting, and flank CNC machining all belong to a class of processes called line-cutting where the cutting tool moves tangentially along the reference geometry. From a geometric point of view, line-cutting brings a unique set of challenges in guaranteeing that the process is collision-free. In this work, given a set of cut-paths on a freeform geometry as the input, we propose a conservative algorithm for finding collision-free tangential cutting directions. These directions, if they exist, are guaranteed to be globally accessible for fabricating the geometry by line-cutting. We then demonstrate how this information can be used to generate globally collision-free cut-paths. We apply our algorithm to freeform models of varying complexity.RYC-2017-2264
Continuous collision detection for ellipsoids
We present an accurate and efficient algorithm for continuous collision detection between two moving ellipsoids. We start with a highly optimized implementation of interference testing between two stationary ellipsoids based on an algebraic condition described in terms of the signs of roots of the characteristic equation of two ellipsoids. Then we derive a time-dependent characteristic equation for two moving ellipsoids, which enables us to develop a real-time algorithm for computing the time intervals in which two moving ellipsoids collide. The effectiveness of our approach is demonstrated with several practical examples. © 2006 IEEE.published_or_final_versio
The Construction of Conforming-to-shape Truss Lattice Structures via 3D Sphere Packing
Truss lattices are common in a wide variety of engineering applications, due to their high ratio of strength versus relative density. They are used both as the interior support for other structures, and as structures on their own. Using 3D sphere packing, we propose a set of methods for generating truss lattices that fill the interior of B-rep models, polygonal or (trimmed) NURBS based, of arbitrary shape. Once the packing of the spheres has been established, beams between the centers of adjacent spheres are constructed, as spline based B-rep geometry. We also demonstrate additional capabilities of our methods, including connecting the truss lattice to (a shell of) the B-rep model, as well as constructing a tensor-product trivariate volumetric representation of the truss lattice - an important step towards direct compatibility for analysis.RYC-2017-2264
Fractal Analysis of Protein Potential Energy Landscapes
The fractal properties of the total potential energy V as a function of time
t are studied for a number of systems, including realistic models of proteins
(PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the
exponent \gamma, is almost independent of temperature and increases with time,
more slowly the larger the protein. Perhaps the most striking observation of
this study is the apparent universality of the fractal dimension, which depends
only weakly on the type of molecular system. We explain this behavior by
assuming that fractality is caused by a self-generated dynamical noise, a
consequence of intermode coupling due to anharmonicity. Global topological
features of the potential energy landscape are found to have little effect on
the observed fractal behavior.Comment: 17 pages, single spaced, including 12 figure
Action-derived molecular dynamics in the study of rare events
We present a practical method to generate classical trajectories with fixed
initial and final boundary conditions. Our method is based on the minimization
of a suitably defined discretized action. The method finds its most natural
application in the study of rare events. Its capabilities are illustrated by
non-trivial examples. The algorithm lends itself to straightforward
parallelization, and when combined with molecular dynamics (MD) it promises to
offer a powerful tool for the study of chemical reactions.Comment: 7 Pages, 4 Figures (3 in color), submitted to Phys. Rev. Let
Synchronous vs. asynchronous dynamics of diffusion-controlled reactions
An analytical method based on the classical ruin problem is developed to
compute the mean reaction time between two walkers undergoing a generalized
random walk on a 1d lattice. At each time step, either both walkers diffuse
simultaneously with probability (synchronous event) or one of them diffuses
while the other remains immobile with complementary probability (asynchronous
event). Reaction takes place through same site occupation or position exchange.
We study the influence of the degree of synchronicity of the walkers and
the lattice size on the global reaction's efficiency. For odd , the
purely synchronous case () is always the most effective one, while for
even , the encounter time is minimized by a combination of synchronous and
asynchronous events. This new parity effect is fully confirmed by Monte Carlo
simulations on 1d lattices as well as for 2d and 3d lattices. In contrast, the
1d continuum approximation valid for sufficiently large lattices predicts a
monotonic increase of the efficiency as a function of . The relevance of the
model for several research areas is briefly discussed.Comment: 21 pages (including 12 figures and 4 tables), uses revtex4.cls,
accepted for publication in Physica
A Doubly Nudged Elastic Band Method for Finding Transition States
A modification of the nudged elastic band (NEB) method is presented that
enables stable optimisations to be run using both the limited-memory
quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV)
minimisers. The performance of this new `doubly nudged' DNEB method is analysed
in conjunction with both minimisers and compared with previous NEB
formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be
quicker by up to two orders of magnitude. Applications to permutational
rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly
cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an
updated algorithm for constructing complicated multi-step pathways using
successive DNEB runs.Comment: 13 pages, 8 figures, 2 table
Constraint methods for determining pathways and free energy of activated processes
Activated processes from chemical reactions up to conformational transitions
of large biomolecules are hampered by barriers which are overcome only by the
input of some free energy of activation. Hence, the characteristic and
rate-determining barrier regions are not sufficiently sampled by usual
simulation techniques. Constraints on a reaction coordinate r have turned out
to be a suitable means to explore difficult pathways without changing potential
function, energy or temperature. For a dense sequence of values of r, the
corresponding sequence of simulations provides a pathway for the process. As
only one coordinate among thousands is fixed during each simulation, the
pathway essentially reflects the system's internal dynamics. From mean forces
the free energy profile can be calculated to obtain reaction rates and insight
in the reaction mechanism. In the last decade, theoretical tools and computing
capacity have been developed to a degree where simulations give impressive
qualitative insight in the processes at quantitative agreement with
experiments. Here, we give an introduction to reaction pathways and
coordinates, and develop the theory of free energy as the potential of mean
force. We clarify the connection between mean force and constraint force which
is the central quantity evaluated, and discuss the mass metric tensor
correction. Well-behaved coordinates without tensor correction are considered.
We discuss the theoretical background and practical implementation on the
example of the reaction coordinate of targeted molecular dynamics simulation.
Finally, we compare applications of constraint methods and other techniques
developed for the same purpose, and discuss the limits of the approach
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