Related papers: Manipulating the motion of large neutral molecules
We study the dynamics of a dimer moving on a periodic one-dimensional substrate as a function of the initial kinetic energy at zero temperature. The aim is to describe, in a simplified picture, the microscopic dynamics of diatomic molecules…
Selected theoretical developments in modeling of deposition of submicrometer size (submicron) particles on solid surfaces, with and without surface diffusion, of interest in colloid, polymer, and certain biological systems, are surveyed. We…
A system of reduced equations is proposed for the electron motion in the strongly-radiation dominated regime for an arbitrary electromagnetic field configuration. The developed approach is used to analyze various scenarios of an electron…
The behavior of nuclear matter is studied at low densities and temperatures using classical molecular dynamics with three different sets of potentials with different compressibility. Nuclear matter is found to arrange in crystalline…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
We study a general problem of the translational/rotational/vibrational/electronic dynamics of a diatomic molecule exposed to an interaction with an arbitrary external electromagnetic field. The theory developed in this paper is relevant to…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,…
We discuss the usefulness of Born-Oppenheimer potential surfaces for nuclear dynamics for molecules strongly coupled to metal surfaces. A simple model demonstrating the construction of such surface for a molecular junction is discussed.
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We present a method to determine the equilibrium geometry of large atomistic systems with linear scaling. It is based on a separate treatment of long and short wavelength components of the forces. While the rapidly varying part is handled…
Micron sized particles are suspended or even lifted up in a gas by thermophoresis. This allows the study of many processes occurring in strongly coupled complex plasmas at the kinetic level in a relatively stress-free environment. First…
Microswimmers and active colloids often move in confined systems, including those involving interfaces. Such interfaces, especially at the microscale, may deform in response to the stresses of the flow created by the active particle. We…
We analyze possible motion control of microparticles by means of external electromagnetic fields which induce potential wells having fixed spatial distribution but deepening over time up to some limit. It is assumed that given particles are…
It is shown that the translational degrees of freedom of a large variety of molecules, from light diatomic to heavy organic ones, can be cooled sympathetically and brought to rest (crystallized) in a linear Paul trap. The method relies on…
Two recent experimental (Li, J.~\emphj{et al}, \emph{Proc.\ Natl.\ Acad.\ Sci.\ U.~S.~A.} {\bf 2014}, 111, 1282-1287) and theoretical studies (B\^aldea, I, \emph{Phys.\ Chem.\ Chem.\ Phys.}\ {\bf 2014}, 16, 25942-25949) have addressed the…
The integration of functional molecules onto conductive or dielectric surfaces represents a promising avenue for employing molecule-centric technologies, encompassing sensor development, electrochromic, and the facilitation of charge and…
It is shown, within classical mechanics, that the field of an electromagnetic vortex is capable of capturing and guiding neutral molecules endowed with a permanent electric dipole moment (PEDM). Similarly as in the case of the magnetic…
Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…
A mechanism for creating well-collimated beams of neutral particles or atoms with spins is studied. The consideration is accomplished for a general realistic case, taking into account: (i) the finiteness of a cylindrical trap where the…