Search results for "Computation"

A density functional theory evaluation of hydrophobic solvation: Ne, Ar and Kr in a 50-water cluster – Implications for the hydrophobic effect

2012

The physical explanation for the hydrophobic effect has been the subject of disagreement. Physical organic chemists tend to use a explanation related to pressure, while many biochemists prefer an explanation that involves decreased entropy of the aqueous solvent. We present DFT calculations at the B3LYP/6-31G(d,p) and X3LYP/6-31G(d,p) levels on the solvation of three noble gases (Ne, Ar, and Kr) in clusters of 50 waters. Vibrational analyses show no substantial decreases in the vibrational entropies of the waters in any of the three clusters. The observed positive free energies of transfer from the gas phase or from nonpolar solvents to water appear to be due to the work needed to make a su…

Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.

2013

ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp…

Antigen recognition by T cells: a strong sense of structure

2001

Conjugacy problem for braid groups and Garside groups

2003

We present a new algorithm to solve the conjugacy problem in Artin braid groups, which is faster than the one presented by Birman, Ko and Lee. This algorithm can be applied not only to braid groups, but to all Garside groups (which include finite type Artin groups and torus knot groups among others).

Chebyshev’s Method on Projective Fluids

2020

We demonstrate the acceleration potential of the Chebyshev semi-iterative approach for fluid simulations in Projective Dynamics. The Chebyshev approach has been successfully tested for deformable bodies, where the dynamical system behaves relatively linearly, even though Projective Dynamics, in general, is fundamentally nonlinear. The results for more complex constraints, like fluids, with a particular nonlinear dynamical system, remained unknown so far. We follow a method describing particle-based fluids in Projective Dynamics while replacing the Conjugate Gradient solver with Chebyshev’s method. Our results show that Chebyshev’s method can be successfully applied to fluids and potentially…

Connected-component identification and cluster update on graphics processing units.

2011

Cluster identification tasks occur in a multitude of contexts in physics and engineering such as, for instance, cluster algorithms for simulating spin models, percolation simulations, segmentation problems in image processing, or network analysis. While it has been shown that graphics processing units (GPUs) can result in speedups of two to three orders of magnitude as compared to serial codes on CPUs for the case of local and thus naturally parallelized problems such as single-spin flip update simulations of spin models, the situation is considerably more complicated for the nonlocal problem of cluster or connected component identification. I discuss the suitability of different approaches…

Representing 2D Digital Objects

2000

The paper describes the combination a multi-views approach to represent connected components of 2D binary images. The approach is based on the Object Connectivity Graph (OCG), which is a sub-graph of the connectivity graph generated by the Discrete Cylindrical Algebraic Decomposition(DCAD) performed in the 2D discrete space. This construction allows us to find the number of connected components, to determine their connectivity degree, and to solve visibility problem. We show that the CAD construction, when performed on two orthogonal views, supply information to avoid ambiguities in the interpretation of each image component. The implementation of the algorithm is outlined and the computati…

Spectral WENO schemes with Adaptive Mesh Refinement for models of polydisperse sedimentation

2012

The sedimentation of a polydisperse suspension with particles belonging to N size classes (species) can be described by a system of N nonlinear, strongly coupled scalar first-order conservation laws. Its solutions usually exhibit kinematic shocks separating areas of different composition. Based on the so-called secular equation [J. Anderson, Lin. Alg. Appl. 246, 49–70 (1996)], which provides access to the spectral decomposition of the Jacobian of the flux vector for this class of models, Burger et al. [J. Comput. Phys. 230, 2322–2344 (2011)] proposed a spectral weighted essentially non-oscillatory (WENO) scheme for the numerical solution of the model. It is demonstrated that the efficiency …

Adaptive mesh reconstruction for hyperbolic conservation laws with total variation bound

2012

We consider 3-point numerical schemes, that resolve scalar conservation laws, that are oscillatory either to their dispersive or anti-diffusive nature. The spatial discretization is performed over non-uniform adaptively redefined meshes. We provide a model for studying the evolution of the extremes of the oscillations. We prove that proper mesh reconstruction is able to control the oscillations; we provide bounds for the Total Variation (TV) of the numerical solution. We, moreover, prove under more strict assumptions that the increase of the TV, due to the oscillatory behavior of the numerical schemes, decreases with time; hence proving that the overall scheme is TV Increase-Decreasing (TVI…

Conservation Laws and Asymptotic Behavior of a Model of Social Dynamics

2008

Abstract A conservative social dynamics model is developed within a discrete kinetic framework for active particles, which has been proposed in [M.L. Bertotti, L. Delitala, From discrete kinetic and stochastic game theory to modelling complex systems in applied sciences, Math. Mod. Meth. Appl. Sci. 14 (2004) 1061–1084]. The model concerns a society in which individuals, distinguished by a scalar variable (the activity) which expresses their social state, undergo competitive and/or cooperative interactions. The evolution of the discrete probability distribution over the social state is described by a system of nonlinear ordinary differential equations. The asymptotic trend of their solutions…