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We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and lambda) using the smotic-suppression technique. Our data are analyzed by revisiting the current theories of DNA packaging in…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
Attention-based Transformers have revolutionized natural language processing (NLP) and shown strong performance in computer vision (CV) tasks. However, as the input sequence varies, the computational bottlenecks in Transformer models…
Synthetic bio-molecular spiders with "legs" made of single-stranded segments of DNA can move on a surface covered by single-stranded segments of DNA called substrates when the substrate DNA is complementary to the leg DNA. If the motion of…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
We present two novel optimizations that accelerate clock-based spiking neural network (SNN) simulators. The first one targets spike timing dependent plasticity (STDP). It combines lazy- with event-driven plasticity and efficiently…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
Given a set of samples, a few of them being possibly saturated, we propose an efficient algorithm in order to cancel saturation while reconstructing band-limited signals. Our method satisfies a minimum-loss constraint and relies on…
We show experimentally that a cheap glass microcapillary can accumulate {\lambda}-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
We recently introduced a fluid-dynamical model for simulating relativistic nuclear collisions in the presence of a first-order phase transition and made explorative studies of head-on lead-lead collisions. We give here a more detailed…
The kinetics of intrinsic and dopant-enhanced solid phase epitaxy (SPE) are stud- ied in buried amorphous Si (a-Si) layers in which SPE is not retarded by H. As, P, B and Al profiles were formed by multiple energy ion implantation over a…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
Stochastic principal component analysis (SPCA) has become a popular dimensionality reduction strategy for large, high-dimensional datasets. We derive a simplified algorithm, called Lazy SPCA, which has reduced computational complexity and…
Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles,…
We investigate the electric double layer formed between charged walls of a slit-like pore and a solvent primitive model (SPM) for electrolyte solution. The recently developed version of the weighted density functional approach for…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…
We study the probability density function (PDF) of the first-reaction times between a diffusive ligand and a membrane-bound, immobile imperfect target region in a restricted "onion-shell" geometry bounded by two nested membranes of…