Related papers: A Rational Method for Probing Macromolecules Disso…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…
A sufficient condition for entanglement in two-mode continuous systems is constructed based on interference visibility and the uncertainty of the total particle number. The observables to be measured (particle numbers and particle number…
This paper presents efficient algorithms for solving the problem of aligning a protein structure template to a query amino-acid sequence, known as protein threading problem. We consider the problem as a special case of graph matching…
We investigate the possibility to determine the divergence-free displacement $\mathbf{u}$ \emph{independently} from the pressure reaction $p$ for a class of boundary value problems in incompressible linear elasticity. If not possible, we…
We apply the multiconfigurational time-dependent Hartree method for indistinguishable particles (MCTDH-X) to systems of bosons or fermions in lattices described by Hubbard type Hamiltonians with long-range or short-range interparticle…
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
A method is presented for tracing the locus of a specific peak in the frequency response under variation of a parameter. It is applicable to periodic, steady-state vibrations of harmonically forced nonlinear mechanical systems. It operates…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations…
The emission of clusters in the nuclear disassembly is investigated within the framework of isospin dependent lattice gas model and classical molecular dynamics model. As observed in the recent experimental data, it is found that the…
The unavoidable coupling of quantum systems to external degrees of freedom leads to dissipative (non-unitary) dynamics, which can be radically different from closed-system scenarios. Such open quantum system dynamics is generally described…
Field-theoretical method is proposed, that yields analytical expression for lateral pressure distribution across hydrophobic core of a bilayer lipid membrane. Lipid molecule, repelling entropicaly surrounding neighbors, is modeled as a…
A novel statistical model for the cooperative binding of monomeric ligands to a linear lattice is developed to study the interaction of ionic surfactant molecules with flexible polyion chain in dilute solution. Electrostatic binding of a…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
We present an efficient approach to the electron correlation problem that is well-suited for strongly interacting many-body systems, but requires only mean-field-like computational cost. %which is based on orbital optimization of electron…
We analyze quantitatively how imaging techniques with single-site resolution allow to measure thermodynamical properties that cannot be inferred from time-of-light images for the trapped Bose-Hubbard model. If the normal state extends over…
Antibodies are widely used in life-sciences and medical therapy. Yet, broadly applicable methods are missing to determine, in the biological system of choice, antibody specificity and its quantitative contribution to e.g. immunofluorescence…
We make the case for studying the complexity of approximately simulating (sampling) quantum systems for reasons beyond that of quantum computational supremacy, such as diagnosing phase transitions. We consider the sampling complexity as a…