Related papers: Single-molecule pulling: phenomenology and interpr…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
Both simple and sophisticated models are frequently used in an attempt to understand how real nuclei breakup when subjected to large excitation energies, a process known as nuclear multifragmentation. Many of these models assume…
Scanning tunneling microscopy (STM) has been a fundamental tool to characterize many-body effects in condensed matter systems, from extended solids to quantum dots. STM of molecules decoupled from the supporting conductive substrate has the…
Clarifying electronic and vibronic properties at individual molecule level provides key insights to future chemistry, nanoelectronics, and quantum information technologies. The single electron tunneling spectroscopy has been used to study…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
We consider the theory of the non-linear spectroscopy for a single molecule undergoing stochastic dynamics and interacting with a sequence of two laser pulses. General expressions for photon counting statistics are obtained, and an exact…
The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our…
Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy…
The transport phenomena of Lennard-Jones molecules through a structural bottleneck driven by an external force are investigated by molecular dynamics simulations. We observe two distinct molecular flow regimes distinguished by a critical…
Molecular electronic devices currently serve as a platform for studying a variety of physical phenomena only accessible at the nanometer scale. One such phenomenon is the highly correlated electronic state responsible for the Kondo effect,…
We carry out experiments on single-molecule junctions at low temperatures, using the mechanically controlled break junction technique. Analyzing the results received with more than ten different molecules the nature of the first peak in the…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging…
In comparing the behavior of an energy spectrum to the predictions of random matrix theory one must transform the spectrum such that the averaged level spacing is constant, a procedure known as unfolding. Once energy spectrums belong to an…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential…