Related papers: The Lennard-Jones Potential Minimization Problem f…
The Lennard-Jones (LJ) Potential Energy Problem is to construct the most stable form of $N$ atoms of a molecule with the minimal LJ potential energy. This problem has a simple mathematical form $f(x) = 4\sum_{i=1}^N \sum_{j=1,j<i}^N…
The simplified Lennard-Jones (LJ) potential minimization problem is $f(x)=4\sum_{i=1}^N \sum_{j=1,j<i}^N (\frac{1}{\tau_{ij}^6} -\frac{1}{\tau_{ij}^3}) {subject to} x\in \mathbb{R}^n,$ where $\tau_{ij}=(x_{3i-2}-x_{3j-2})^2…
X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are two powerful tools to determine the protein 3D structure. However, not all proteins can be successfully crystallized, particularly for membrane proteins. Although…
Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);…
In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and…
X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are two powerful tools to determine the protein 3D structure. However, not all proteins can be successfully crystallized, particularly for membrane proteins. Although…
X-ray crystallography is a powerful tool to determine the protein 3D structure. However, it is time-consuming and expensive, and not all proteins can be successfully crystallized, particularly for membrane proteins. Although nuclear…
To the best of the author's knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the unstable, noncrystalline and insoluble nature of the amyloid…
We study the two dimensional Lennard-Jones energy per particle of lattices and we prove that the minimizer among Bravais lattices with sufficiently large density is triangular and that is not the case for sufficiently small density. We give…
Good a-priori bounds on the smallest pairwise distance $r_{\rm{{min}}}(\mbox{LJ}_N^{\rm{gmin}})$ for a three-dimensional (3D) Lennard-Jones $N$-body cluster of globally minimal energy can significantly reduce the computational search space…
It is well-known that any Lennard-Jones type potential energy must have a periodic ground state given by a triangular lattice in dimension 2. In this paper, we describe a computer-assisted method that rigorously shows such global minimality…
Many experimental studies have shown that the prion AGAAAAGA palindrome hydrophobic region (113-120) has amyloid fibril forming properties and plays an important role in prion diseases. However, due to the unstable, noncrystalline and…
The Lennard-Jones 12-6 potential (LJ) is arguably the most widely used pair potential in Molecular Simulations. In fact, it is so popular that the question is rarely asked whether it is fit for purpose. In this paper, we argue that, whilst…
The reconstruction of low-rank matrix from its noisy observation finds its usage in many applications. It can be reformulated into a constrained nuclear norm minimization problem, where the bound $\eta$ of the constraint is explicitly given…
he segment minimization problem consists of finding the smallest set of integer matrices that sum to a given intensity matrix, such that each summand has only one non-zero value, and the non-zeroes in each row are consecutive. This has…
We consider an $\ell_0$-minimization problem where $f(x) + \gamma \|x\|_0$ is minimized over a polyhedral set and the $\ell_0$-norm regularizer implicitly emphasizes sparsity of the solution. Such a setting captures a range of problems in…
We present a new theoretical framework for modelling the fusion process of Lennard-Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we…
In this contribution we are concerned with efficient model reduction for multiscale problems arising in lithium-ion battery modeling with spatially resolved porous electrodes. We present new results on the application of the reduced basis…
In this paper, we study minimization problems among Bravais lattices for finite energy per point. We prove that if a function is completely monotonic, then the triangular lattice minimizes energy per particle among Bravais lattices with…
In this paper we consider three minimization problems, namely quadratic, $\rho$-convex and quadratic fractional programing problems. The quadratic problem is considered with quadratic inequality constraints with bounded continuous and…