Related papers: Improving signal-to-noise resolution in single mol…
We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
In this work we study the detection of weak stimuli by spiking neurons in the presence of certain level of noisy background neural activity. Our study has focused in the realistic assumption that the synapses in the network present…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are…
Dual trap optical tweezers are often used in high-resolution measurements in single-molecule biophysics. Such measurements can be hindered by the presence of extraneous noise sources, the most prominent of which is the coupling of…
Physical transceivers have hardware impairments that create distortions which degrade the performance of communication systems. The vast majority of technical contributions in the area of relaying neglect hardware impairments and, thus,…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Object This study demonstrates the applicability of semi-LASER localized dynamic $^{31}$P MRS to deeper lying areas of the exercising human soleus muscle (SOL). The effect of accurate localization and high temporal resolution on data…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
Spiking neural networks (SNNs) have closer dynamics to the brain than current deep neural networks. Their low power consumption and sample efficiency make these networks interesting. Recently, several deep convolutional spiking neural…
We investigate methods for experimental performance enhancement of auto-encoders based on a recurrent neural network (RNN) for communication over dispersive nonlinear channels. In particular, our focus is on the recently proposed sliding…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
Ensuring the stability of the AuNP-gene complex until it reaches the target sites is a crucial factor for the success of gene therapy. Though different AuNP sizes and AuNP-to-DNA ratios are investigated for specific therapeutic needs, their…
In a typical single molecule experiment, dynamics of an unfolded proteins is studied by determining the reconfiguration time using long-range Forster resonance energy transfer where the reconfiguration time is the characteristic decay time…
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…