All posts under tag "Condensed Matter"
We show that the Boltzmann factor has a geometrical origin. Its derivation follows from the microcanonical picture. The Maxwell-Boltzmann distribution or the wealth distribution in human society are some direct applications of this new interpretation.
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We analyze extensive simulation data of an alpha-helix in expli
Fibered confocal fluorescence microscopy (FCFM) is a new technique that can be used during a bronchoscopy to analyze the nature of the human bronchial and alveolar mucosa fluorescence microstructure. An endoscopic fibered confocal fluorescence microscopy system with spectroscopic analysis capability
In this paper we study Inozemtsev's su(m) quantum spin model with hyperbolic interactions and the associated spin chain of Haldane-Shastry type introduced by Frahm and Inozemtsev. We compute the spectrum of Inozemtsev's model, and use this result and the freezing trick to derive a simple analytic ex
We consider a strongly interacting ${}^{6}$Li-${}^{40}$K mixture, which is imbalanced both in the masses and the densities of the two fermionic species. At present, it is the experimentalist's favorite for reaching the superfluid regime. We construct an effective thermodynamic potential that leads t
Much attention has been focused on the design of low barrier nanomagnets (LBM), whose magnetizations vary randomly in time owing to thermal noise, for use in binary stochastic neurons (BSN) which are hardware accelerators for machine learning. The performance of BSNs depend on two important paramete
Biodiversity is essential to the viability of ecological systems. Species diversity in ecosystems is promoted by cyclic, non-hierarchical interactions among competing populations. Such non-transitive relations lead to an evolution with central features represented by the `rock-paper-scissors' game,
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing environment. Programmed adaptation to the same universal law for no
Irreversible opinion spreading phenomena are studied on small-world networks generated from 2D regular lattices by means of the magnetic Eden model, a nonequilibrium kinetic model for the growth of binary mixtures in contact with a thermal bath. In this model, the opinion or decision of an individua
In this work we present a general mechanism by which simple dynamics running on networks become self-organized critical for scale free topologies. We illustrate this mechanism with a simple arithmetic model of division between integers, the division model. This is the simplest self-organized critica
An efficient low-order scaling method is presented for large-scale electronic structure calculations based on the density functional theory using localized basis functions, which directly computes selected elements of the density matrix by a contour integration of the Green function evaluated with a
In this paper, we consider the volume enclosed by the microcanonical ensemble in phase space as a statistical ensemble. This can be interpreted as an intermediate image between the microcanonical and the canonical pictures. By maintaining the ergodic hypothesis over this ensemble, that is, the equip
In an informal way, a number of thoughts on the financial crisis 2008 are presented from a physicist's viewpoint, considering the problem as a nonergodicity transition of a spin-glass type of system. Some tentative suggestions concerning the way out of the crisis are also discussed, concerning Keyne
Standard density functional approximations greatly over-estimate the static polarizability of longchain polymers, but Hartree-Fock or exact exchange calculations do not. Simple self-interaction corrected (SIC) approximations can be even better than exact exchange, while their computational cost can
Room temperature angle-dispersive x-ray diffraction measurements on spinel ZnGa2O4 up to 56 GPa show evidence of two structural phase transformations. At 31.2 GPa, ZnGa2O4 undergoes a transition from the cubic spinel structure to a tetragonal spinel structure similar to that of ZnMn2O4. At 55 GPa, a
We document our Fortran 77 code for multicanonical simulations of 4D U(1) lattice gauge theory in the neighborhood of its phase transition. This includes programs and routines for canonical simulations using biased Metropolis heatbath updating and overrelaxation, determination of multicanonical weig
RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the steric interactions of the RNAPs and their mechanochemical cycl
Orbital-free (OF) methods promise significant speed-up of computations based on density functional theory (DFT). In this field, the development of accurate kinetic-energy density functionals remains an open question. In this chapter we review the shell-correction method (SCM, commonly known as Strut
We study a trapped system of fermions with a zero-range two-body interaction using the shell-model Monte Carlo method, providing {em ab initio} results for the low particle number limit where mean-field theory is not applicable. We present results for the $N$-body energies as function of interaction
We describe the hardwired implementation of algorithms for Monte Carlo simulations of a large class of spin models. We have implemented these algorithms as VHDL codes and we have mapped them onto a dedicated processor based on a large FPGA device. The measured performance on one such processor is co
The stability of the dynamical states characterized by a uniform firing rate ({it splay states}) is analyzed in a network of globally coupled leaky integrate-and-fire neurons. This is done by reducing the set of differential equations to a map that is investigated in the limit of large network size.
During the synthesis of integral membrane proteins (IMPs), the hydrophobic amino acids of the polypeptide sequence are partitioned mostly into the membrane interior and hydrophilic amino acids mostly into the aqueous exterior. We analyze the minimum free energy state of polypeptide sequences partiti
We study the susceptibility propagation, a message-passing algorithm to compute correlation functions. It is applied to constraint satisfaction problems and its accuracy is examined. As a heuristic method to find a satisfying assignment, we propose susceptibility-guided decimation where correlations
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can be minimized, under selective pressure, by adjusting the sp
The eye lens is the most characteristic example of mammalian tissues exhibiting complex colloidal behaviour. In this paper we briefly describe how dynamics in colloidal suspensions can help addressing selected aspects of lens cataract which is ultimately related to the protein self-assembly under pa
The missing piece in the jigsaw of silicon photonics is a light source that can be easily incorporated into the standard silicon fabrication process. Recent advances in the development of atomically thin layers of semiconducting transition metal dichalogenides (TMDs), with direct bandgaps in the nea
Room-temperature (RT) Pulsed Cathodoluminescence (PCL) spectra of a set of pure synthetic (both crystalline and amorphous) silicon dioxide materials were studied. It is shown, that the PCL spectra of all samples (both amorphous and crystalline) possess a separate band at 495 nm (2.5 eV). This band i
We present an improved parallel algorithm for the enumeration of fixed benzenoids B_h containing h hexagonal cells. We can thus extend the enumeration of B_h from the previous best h=35 up to h=50. Analysis of the associated generating function confirms to a very high degree of certainty that $B_h s
The adsorption behavior of toxic gas molecules (NO, CO, NO2, and NH3) on graphene-like BC3 are investigated using first-principle density functional theory (DFT). The most stable adsorption configurations, adsorption energies,binding distances,charge transfers,electronic band structures,and the cond
A quite general device analysis method that allows the direct evaluation of optical and recombination losses in crystalline silicon (c-Si)-based solar cells has been developed. By applying this technique, the optical and physical limiting factors of the state-of-the-art solar cells with ~20% efficie
Futures trading is the core of futures business, and it is considered as one of the typical complex systems. To investigate the complexity of futures trading, we employ the analytical method of complex networks. First, we use real trading records from the Shanghai Futures Exchange to construct futur
Genetic robustness, the preservation of an optimal phenotype in the face of mutations, is critical to the understanding of evolution as phenotypically expressed genetic variation is the fuel of natural selection. The origin of genetic robustness, whether it evolves directly by natural selection or i
We examine the effective counterion-mediated electrostatic interaction between two like-charged dielectric cylinders immersed in a continuous dielectric medium containing neutralizing mobile counterions. We focus on the effects of image charges induced as a result of the dielectric mismatch between
We report on the interfacial electronic properties of HfO2 gate dielectrics both, with GaN towards normally-OFF recessed HEMT architectures and the AlGaN barrier for normally-ON AlGaN/GaN MISHEMTs for GaN device platforms on Si. A conduction band offset of 1.9 eV is extracted for HfO2/GaN along with
We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that follows the geometry defined by atomistic data. On this mesh, diff
We investigate the slow time scales that arise from aging of the paths during the process of path aggregation. This is studied using Monte-Carlo simulations of a model aiming to describe the formation of fascicles of axons mediated by contact axon-axon interactions. The growing axons are represented
Molecular-dynamics algorithms for systems of particles interacting through discrete or 'hard' potentials are fundamentally different to the methods for continuous or 'soft' potential systems. Although many software packages have been developed for continuous potential systems, software for discrete
Monolayer two-dimensional transitional metal dichalcogenides, such as MoS2, WS2 and WSe2, are direct band gap semiconductors with large exciton binding energy. They attract growing attentions for opto-electronic applications including solar cells, photo-detectors, light-emitting diodes and photo-tra
Voltage control effects provide an energy-efficient means of tailoring material properties, especially in highly integrated nanoscale devices. However, only insulating and semiconducting systems can be controlled so far. In metallic systems, there is no electric field due to electron screening effec
To ensure the practical application of atomically thin transition metal dichalcogenides, it is essential to characterize their structural stability under external stimuli such as electric fields and currents. Using vacancy monolayer islands on TiSe2 surfaces as a model system, for the first time we
Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self ener
Boltzmann's struggle with a derivation of the Second Law of Thermodynamics is sketched. So is his first derivation of the connection between entropy and probability in 1877. Planck's derivation and quantum mechanical modifications of Boltzmann's connection between entropy probability are given next.
The focus of this article is on entropy and Markov processes. We study the properties of functionals which are invariant with respect to monotonic transformations and analyze two invariant 'additivity' properties: (i) existence of a monotonic transformation which makes the functional additive with r
The possibility of hybridizing collective electronic motion with mid-infrared (mid-IR) light to form surface polaritons has made van der Waals layered materials a versatile platform for extreme light confinement and tailored nanophotonics. Graphene and its heterostructures have attracted particular
We study a directed flipping process that underlies the performance of the random edge simplex algorithm. In this stochastic process, which takes place on a one-dimensional lattice whose sites may be either occupied or vacant, occupied sites become vacant at a constant rate and simultaneously cause
We report a gas eruption phenomenon caused by electrolysis of liquid Ga-In alloy in an electrolyte, especially NaOH solution. A volcanic eruption-like blowout of gas occurred from the orifice on the alloy surface. In addition to gas plume, large gas bubbles were also generated and the total gas yiel
The exceptional conducting nature of graphene makes it a viable candidate for enhancing the effectiveness of photocatalytic and biomedical nanomaterials. Herein, the immobilization of monodispersed silicon dioxide (SiO2) nanoparticles on multiple graphene layers is demonstrated for intercalation of
Experiments, numerical simulations and an analytic model were developed to elucidate the effects of noise in the synchronized state of a tunnel junction based spin torque nano oscillator (STNO). It is demonstrated that in the in plane magnetized structure, while the frequency is locked, much higher
Investigating the interaction of electron beams with materials and light has been a field of research since more than a century. The field was advanced theoretically by the raise of quantum mechanics and technically by the introduction of electron microscopes and accelerators. It is possible nowaday
Numerical models indicate that collective animal behaviour may emerge from simple local rules of interaction among the individuals. However, very little is known about the nature of such interaction, so that models and theories mostly rely on aprioristic assumptions. By reconstructing the three-dime
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