Related papers: A Rational Method for Probing Macromolecules Disso…
In lattice QCD, both direct method and HAL QCD method are used to investigate the two-baryon systems. We show that due to the contamination of the scattering excited states, it is challenging to measure the eigenenergy from the temporal…
Asymptotic homogenisation is used to systematically derive reduced-order macroscopic models of conductive behaviour in spirally-wound layered materials in which the layers have very different conductivities. The problem is motivated by the…
Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We present a framework for discriminative sequence classification where the learner works directly in the high dimensional predictor space of all subsequences in the training set. This is possible by employing a new coordinate-descent…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
The Cahn-Hilliard system has been used to describe a wide number of phase separation processes, from co-polymer systems to lipid membranes. In this work the convergence properties of a closest-point based scheme is investigated. In place of…
Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity…
In this work we consider the elasticity problem for two domains separated by a heterogeneous layer. The layer has an $\varepsilon-$periodic structure, $\varepsilon\ll1$, including a multiple micro-contact between the structural components.…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the…
In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated…
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…
The present manuscript revisits one of the earliest approaches to treating molecular systems within the Schr\"odinger formalism of quantum mechanics: the Heitler-London (HL) model. Originally proposed in 1927 and based on a linear…
We consider the photodissociation of ground-state bosonic molecules trapped in an optical lattice potential into two-component fermionic atoms. The system is assumed to be described by a one-band resonantly-coupled Bose-Fermi Hubbard model.…
In a recent paper [PRL 91, 138103 (2003)] a new mechanism to explain the cold denaturation of proteins, based on the loss of local low-density water structure, has been proposed. In the present paper this mechanism is tested by means of…
The large body of experimental data on nuclear fission is analyzed with a semi-empirical ordering scheme based on the macro-microscopic approach and the separability of compound-nucleus and fragment properties on the fission path. We apply…
The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality…