相关论文: Excluded Volume in Protein Sidechain Packing
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
For a $d$-dimensional random vector $X$, let $p_{n, X}(\theta)$ be the probability that the convex hull of $n$ independent copies of $X$ contains a given point $\theta$. We provide several sharp inequalities regarding $p_{n, X}(\theta)$ and…
We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to…
The spatial correlations of entangled polymer dynamics are examined by molecular dynamics simulations and neutron spin-echo spectroscopy. Due to the soft nature of topological constraints, the initial spatial decays of intermediate…
An elastoplastic theory is not volume conserved if it improperly sets an arbitrary plastic strain rate tensor to be deviatoric. This paper discusses how to rigorously realize volume conservation in finite strain regime, especially when the…
Scaling predictions and results from self-consistent field calculations for bottle-brush polymers with a rigid backbone and flexible side chains under good solvent conditions are summarized and their validity and applicability is assessed…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Herein, we propose a site random cluster model by introducing an additional cluster weight in the partition function of the traditional site percolation. To simulate the model on a square lattice, we combine the color-assignation and the…
Mean-field techniques provide a rather accurate description of single-chain conformations in spatially inhomogeneous polymer systems containing interfaces or surfaces. Intermolecular correlations, however, are not described by the…
Sheet cavitation appears in many hydraulic applicationss and can lead to technical issues. Some fundamental outcomes such as the complex topology of 3-Dimensional cavitation pockets and their associated dynamics need to be carefully…
The volume entropy of a compact metric measure space is known to be the exponential growth rate of the measure lifted to its universal cover at infinity. For a compact Riemannian $n$-manifold with a negative lower Ricci curvature bound and…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the…
For points $p_1,\ldots , p_n$ in the unit square $[0,1]^2$, an \emph{anchored rectangle packing} consists of interior-disjoint axis-aligned empty rectangles $r_1,\ldots , r_n\subseteq [0,1]^2$ such that point $p_i$ is a corner of the…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
When compressed in a slit of width $D$, a $\Theta$-chain that displays the scaling of size $R_0$ (diameter) with respect to the number of monomers $N$, $R_0\sim aN^{1/2}$, expands in the lateral direction as $R_{\parallel}\sim a…
Calculating the vibrational entropy of an N-atom assembly in the harmonic approximation requires the diagonalisation of a large matrix. This operation becomes rapidly time consuming when increasing the dimensions of the simulation cell. In…