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This computational research study analyzes the increase of the specific charge capacity that comes with the reduction of the anisotropic volume expansion during lithium ion insertion within silicon nanowires. This research paper is a…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
The transport of fluids at the nanoscale is fundamental to manifold biological and industrial processes, ranging from neurotransmission to ultrafiltration. Yet, it is only recently that well-controlled channels with cross-sections as small…
We discuss the extension of the empirical equation: $\left\langle s_{N}^{2}\right\rangle_{0}\propto g\,l^{2}$, where the subscript 0 denotes the ideal value with no excluded volume and $g$ the generation number from the root to the youngest…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
On the basis of the thermodynamic theory of the excluded volume effects, we show that the size exponent varies abruptly, depending on the change of the segment concentration. For linear polymers, the exponent changes discontinuously from…
Gene expression via transcription-translation is the most fundamental reaction to sustain biological systems, and complex reactions such as this one occur in a small compartment of living cells. There is increasing evidence that t physical…
We report the splitting of an oscillating DNA circuit into $\sim 700$ droplets with picoliter volumes. Upon incubation at constant temperature, the droplets display sustained oscillations that can be observed for more than a day.…
Ion transport measurements are widely used as an indirect probe for various properties of confined electrolytes. It is generally assumed that the ion concentration in a nanoscale channel is equal to the ion concentration in the macroscopic…
We report a theoretical study of ion size effect on various properties in a soft nanochannel with pH-dependent charge density. We develop a free energy based mean-field theory taking into account ion size as well as pH-dependence of charged…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic…
Molecular weight dependence of excluded volume effects is examined. The swollen-to-unperturbed coil transition point shifts to lower concentration range with increasing molecular weight (Mw). It is shown that in the limit of the infinite…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
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…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
The short diffusion lengths in insertion battery nanoparticles render the capacitive behavior of bounded diffusion, which is rarely observable with conventional larger particles, now accessible to impedance measurements. Coupled with…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…