Related papers: A simple electrostatic model applicable to biomole…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Relaxing the assumption of "infinite and homogenous background" the dielectric response function of one-dimensional (1D) semiconducting nanowires embedded in a dielectric environment is calculated. It is shown that high-k (higher than…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
We simulate model systems of charged spherical particles in their counterion solution and measure the thermodynamic pressure and the pair distribution function from which we derive effective potentials of mean force. For a system with only…
When a $\gamma$-ray interacts in a semiconductor detector, the resulting electron-hole charge clouds drift towards their respective electrodes for signal collection. These charge clouds will expand over time due to both thermal diffusion…
Electrostatic repulsions can drive crystallization in many-particle systems. For charged colloidal systems, the phase boundaries as well as crystal structure are highly tunable by experimental parameters such as salt concentration and pH.…
We describe two different modes for electronically detecting an adsorbed molecule using a nanoscale transistor. The attachment of an ionic molecular target shifts the threshold voltage through modulation of the depletion layer…
By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
The purpose of this project is to investigate the use of charge couple devices (CCDs) to detect electrons directly. This can be done in transmission electron microscopy (TEM) for electrons over 100 KeV, but for space plasma instruments,…
The experimentally observed swelling and collapse response of weakly charged polymers to the addition of specific salts displays quite convoluted behavior that is not easy to categorize. Here we use a minimalistic implicit solvent /…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…
Within the problem of the finding of the mean potential energy of the charged particle in the plasma in this work a classification of physical systems (electrolytes, dusty plasmas, plasmas) is made based on consideration, or lack thereof,…
We consider dipolar interactions between heteronuclear molecules in a low-dimensional setup consisting of two one-dimensional tubes. We demonstrate that attraction between molecules in different tubes can overcome intratube repulsion and…
We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our…
This paper constructs dynamical models and estimation algorithms for the concentration of target molecules in a fluid flow using an array of novel biosensors. Each biosensor is constructed out of protein molecules embedded in a synthetic…
Motivated by the need for less destructive imaging of nanostructures, we pursue point-source in-line holography (also known as point projection microscopy, or PPM) with very low energy electrons (-100 eV). This technique exploits the recent…