Related papers: Force Feedback Effects on Single Molecule Hopping …
In this work we propose an extension to the analytical one-dimensional model proposed by E. Gnecco (Phys. Rev. Lett. 84:1172) to describe friction. Our model includes normal forces and the dependence with the angular direction of movement…
We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This "Landauer-B\"uttiker's probe technique" can properly…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
The role of interchain hopping in quasi-one-dimensional (Q-1D) electron systems is investigated by extending the Kadanoff-Wilson renormalization group of one-dimensional (1D) systems to Q-1D systems. This scheme is applied to the extended…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
Quantum technologies and experiments often require preparing systems in low-temperature states. Here, we investigate cooling schemes using feedback protocols modeled with a Quantum Fokker-Planck Master Equation (QFPME) recently derived by…
Atoms or pairs of ions picked up by probe tips used in dynamic force microscopy (DFM) can be strongly displaced and even hop discontinuously upon approach to the sample surface. The energy barriers for some of those hops are of the right…
Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…
The potential of mean force (PMF) between two nano crystals (NCs) represents an effective interaction potential that can be used to study the assembly of NCs to various superstructures. For a given temperature, the effective interaction is…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
In particle systems subject to a nonuniform drive, particle migration is observed from the driven to the non--driven region and vice--versa, depending on details of the hopping dynamics, leading to apparent violations of Fick's law and of…
Molecular dynamic (MD) simulations are applied to investigate the dependency of the kinetic friction coefficient on the temperature at the nano-scale. The system is comprised of an aluminum spherical particle consisting of 32000 atoms in an…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…
Single-molecule stretching experiments on DNA, RNA, and other biological macromolecules opened up the possibility of an impressive progress in many fields of Life and Medical sciences. The reliability of such experiments may be crucially…
We demonstrate a new feedback algorithm to cool a single neutral atom trapped inside a standing-wave optical cavity. The algorithm is based on parametric modulation of the confining potential at twice the natural oscillation frequency of…
The description of nonequilibrium processes in nano-sized objects, where the typical energies involved are a few times, is increasingly becoming central to disciplines as diverse as condensed-matter physics, materials science, and…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…