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The field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. Thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which…
A proximity-effect thermometer measures the temperature dependent critical supercurrent in a long superconductor - normal metal - superconductor (SNS) Josephson junction. Typically, the transition from the superconducting to the normal…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
We consider the thermal breakage of a tethered polymer chain of discrete segments coupled by Morse potentials under constant tensile stress. The chain dynamics at the onset of fracture is studied analytically by Kramers-Langer…
The formation of liquid bridges between a planar and conical substrates is analyzed macroscopically taking into account the line tension. Depending on the value of the line tension coefficient \tau and geometric parameters of the system one…
We have investigated several ultra-thin copper nanobridges between supporting layers using a classical molecular dynamics simulation and a many-body potential function of the second-moment approximation of tight-binding scheme. This…
Molecular dynamics simulations are used to assess the influence of Coulomb coupling on the energy evolution of charged projectiles in the classical one-component plasma. The average projectile kinetic energy is found to decrease linearly…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
A scanning tunneling microscope (STM) supplemented with a force sensor is used to study the mechanical properties of a novel metallic nanostructure: a freely suspended chain of single gold atoms. We find that the bond strength of the…
This paper examines the effect of temperature on the structural stability and mechanical properties of 20 layered (10,10) single walled carbon nanotubes (SWCNTs) under tensile loading using an O(N) tight binding molecular dynamics (TBMD)…
In this chapter, we illustrate recently obtained thermodynamic bounds for a number of enzymatic networks by focusing on simple examples of unicyclic or multi-cyclic networks. We also derive complementary relations which constrain the…
Inspired by the work of Kamenev and Kohn, we present a general discussion of the two-terminal dc conductance of molecular devices within the framework of Time Dependent Current-Density Functional Theory. We derive a formally exact…
We investigate the thermoelectric response of single-molecule junctions composed of acyclic cross-conjugated molecules, including dendralene analogues and related iso-poly(diacetylene) (iso-PDA) motifs, in which node-possessing repeat units…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
Using a statistical mechanical model and numerical simulations, we provide the design principle for the bridging strength ($\xi$) and linker density ($\rho$) dependent superselectivity in linker-mediated multivalent nanoparticle adsorption.…
We predict an enormous order-dependent quantum enhancement of thermoelectric effects in the vicinity of a higher-order `supernode' in the transmission spectrum of a nanoscale junction. Single-molecule junctions based on 3,3'-biphenyl and…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
When a small system is coupled to a bath, it is generally assumed that the state of the bath remains unaffected by the system due to the bath's large number of degrees of freedom. Here we show theoretically that this assumption can be…