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We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new insights into the mechanisms of self-organization in bacterial cells and indicate... |
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials applications. |
Recent findings raise the possibility of PARP inhibitor therapy in colorectal cancers(CRCs). However, the extent of PARP-1 protein expression in clinical specimens of CRC is not known. |
Biochemical reaction systems in mesoscopic volume, under sustained environmental chemical gradient(s), can have multiple stochastic attractors. Two distinct mechanisms are known for their origins: ($a$) Stochastic single-molecule events, such as gene expression, with slow gene on-off dynamics; and ($b$) nonlinear netw... |
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the coding sequence of the huntingtin protein. Initially, it predominantly affects medium-sized spiny neurons (MSSNs) of the corpus striatum. |
Keratin are among the most abundant proteins in epithelial cells. Functions of the keratin network in cells are shaped by their dynamical organization. |
Intermediate filaments form an essential structural network, spread throughout the cytoplasm and play a key role in cell mechanics, intracellular organization and molecular signaling. The maintenance of the network and its adaptation to the cell's dynamic behavior relies on several mechanisms implicating cytoskele... |
Symmetry breaking, a central principle of physics, has been hailed as the driver of self-organization in biological systems in general and biogenesis of cellular organelles in particular, but the molecular mechanisms of symmetry breaking only begin to become understood. Centrioles, the structural cores of centrosomes ... |
Turgor is the driving force of plant growth, making possible for roots to overcome soil resistance or for stems to counteract gravity. Maintaining a constant growth rate while avoiding the cell content dilution, which would progressively stop the inward water flux, imposes the production or import of osmolytes in prop... |
We address the controversial hot question concerning the validity of the loose coupling versus the lever-arm theories in the actomyosin dynamics by re-interpreting and extending the phenomenological washboard potential model proposed by some of us in a previous paper. In this new model a Brownian motion harnessing the... |
A major open problem in biophysics is to understand the highly heterogeneous transport of many structures inside living cells, such as endosomes. We find that mathematically it is described by spatio-temporal heterogeneous fractional Brownian motion (hFBM) which is defined as FBM with a randomly switching anomalous ex... |
RNA thermometers are mRNA strands with a temperature dependent secondary structure: depending on the spatial conformation, the mRNA strand can get translated (on-state) or can be inaccessible for ribosomes binding (off-state). These have been found in a number of microorganisms (mainly pathogens), where they are used ... |
The multiple worlds of genetically manipulated laboratory organisms such as transgenic mice or worms with certain gene mutations are somewhat reminiscent of parallel worlds in quantum mechanics. So are various models of aging tested in such organisms. |
Motor proteins that specifically interact with the ends of cytoskeletal filaments can induce filament depolymerization. A phenomenological description of this process is presented. |
The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth and survival. Sensory adaptation allows a cell to recover its sensitivity after a transient response to a shift in the strength of extracellular stimulus. |
We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability that extends down to zero wavevector, connecting at that point to two symmetry modes of the underlying dynamical system. |
We focused our attention on Ca$^{2+}$ release from the endoplasmic reticulum through a cluster of inositol 1,4,5-trisphosphate (IP$_3$) receptor channels. The random opening and closing of these receptors introduce stochastic effects that have been observed experimentally. |
Telomeres, the nucleoprotein complexes at the termini of linear chromosomes, are essential for the processes of end replication, end-protection, and chromatin segregation. The Mre11 complex is involved in multiple cellular roles in DNA repair and structure in the regulation and function of telomere size homeostasis. |
Many cellular processes are tightly connected to the dynamics of microtubules (MTs). While in neuronal axons MTs mainly regulate intracellular trafficking, they participate in cytoskeleton reorganization in many other eukaryotic cells, enabling the cell to efficiently adapt to changes in the environment. |
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the nascent RNA numbers. |
Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and bidirectional transport of intracellular cargo over long distances. |
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the cause-effect relationships. |
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. |
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. |
Mutations in the MTM1 gene, encoding the phosphoinositide phosphatase myotubularin, are responsible for the X-linked centronuclear myopathy (XLCNM) or X-linked myotubular myopathy (XLMTM). The MTM1 gene was first identified in 1996 and its function as a PtdIns3P and PtdIns(,5)P2 phosphatase was discovered in 2000. |
Protein tagging with CRISPR-Cas9 enables the investigation of protein function in its native environment but is limited by low homology-directed repair (HDR) efficiency causing low knock-in rates. We present a detailed pipeline using HDR donor plasmids containing antibiotic resistance cassettes for rapid selection of ... |
The number of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy model to study the trade-off between the ribosomal supply and the demand of the translation machinery, dictated by the composition of the transcript... |
We investigate the cooperative dynamics of an ensemble of N microtubules growing against an elastic barrier. Microtubules undergo so-called catastrophes, which are abrupt stochastic transitions from a growing to a shrinking state, and rescues, which are transitions back to the growing state. |
The dynamics of two groups of molecular motors pulling in opposite directions on a rigid filament is studied theoretically. To this end we first consider the behavior of one set of motors pulling in a single direction against an external force using a new mean-field approach. |
The Cooper pairs in superconducting condensates are shown to acquire a temperature-dependent dc magnetic moment under the effect of the circularly polarized electromagnetic radiation. The mechanisms of this inverse Faraday effect are investigated within the simplest version of the phenomenological dynamic theory for s... |
We study the emergence of charge ordered phases within a pi-loop current (piLC) model for the pseudogap based on a three-band model for underdoped cuprate superconductors. Loop currents and charge ordering are driven by distinct components of the short-range Coulomb interactions: loop currents result from the repulsio... |
We study the effect of U=0 impurities on the superconducting and thermodynamic properties of the attractive Hubbard model on a square lattice. Removal of the interaction on a critical fraction of $f_{\rm crit} \approx 0.30$ of the sites results in the destruction of off-diagonal long range order in the ground state. |
Low-temperature variable-energy electron irradiation was used to induce non-magnetic disorder in a single crystal of hole-doped iron-based superconductor, Ba$_{1-x}$K$_x$Fe$_2$As$_2$, $x=$0.80. To avoid systematic errors, the beam energy was adjusted non-consequently for five values between 1.0 and 2.5 MeV, whence sam... |
With the ever-increasing energy need to process big data, the realization of low-power computing technologies, such as superconducting logic and memories, has become a pressing issue. Developing fast and non-volatile superconducting memory elements, however, remains a challenge. |
The maximum value of the energy gap $\Delta\simeq 8\ meV$ and the ratio $2\delta/kT_c\simeq~2.5$ are determined for a high-temperature superconductor $\rm Bi_2Sr_2CaCu_2O_{8+y}$ by using point contacts. It was found that the high-temperature superconductor is transformed under the effect of current injection of quasip... |
Although copper and bismuth do not form any compounds at ambient conditions, two intermetallics, CuBi and Cu$_{11}$Bi$_7$, were recently synthesized at high pressures. Here we report on the discovery of additional copper-bismuth phases at elevated pressures with high-densities from ab initio calculations. |
Sc5Rh6Sn18 with a cage-type quasiskutterudite crystal lattice and type II superconductivity, with superconducting transition temperature Tc = 4.99 K, was investigated under hydrostatic high-pressure (HP) using electrical transport, synchrotron X-ray diffraction (XRD) and Raman spectroscopy. Our data show that HP enhan... |
A recent experiment reported that robust superconductivity appears in NbTi alloys under ultrahigh pressures with an almost constant superconducting $T_c$ of ~19 K from 120 to 261.7 GPa [J. Guo et al., Adv. Mater. 31, 1807240 (2019)], which is very rare among the known superconductors. We investigate the origin of this... |
The advent of high transverse-field muon spin rotation (TF-muSR) has led to recent muSR investigations of the magnetic-field response of cuprates above the superconducting transition temperature T_c. Here the results of such experiments on hole-doped cuprates are reviewed. |
We report resonant electronic Raman scattering in optimally doped single layer HgBa$_2$CuO$_{4+\delta}$ (Hg-1201) and trilayer HgBa$_2$Ca$_2$Cu$_3$O$_{8+\delta}$ (Hg-1223) single crystals. Analysis of the $B_{1g}$ and B$_{2g}$ channels in the superconducting state of Hg-1201 advocates for a gap having d-wave symmetry.... |
Josephson junctions containing two ferromagnetic layers are being considered for use in cryogenic memory. Our group recently demonstrated that the ground-state phase difference across such a junction with carefully chosen layer thicknesses could be controllably toggled between zero and $\pi$ by switching the relative ... |
Numerical studies of the flux creep in superconductors show that the distribution of the magnetic field at any stage of the creep process can be well described by the condition of spatial constancy of the activation energy $U$ independently on the particular dependence of $U$ on the field B and current $j$. This resul... |
This paper examines the micro-parameters of superconductors. It studies the modulations from weak van der Waals interaction to strong covalence bonding of superconductors. |
We report results of experiments with liquid $^3$He confined in a high porosity anisotropic nanostructure which we call planar aerogel. This aerogel consists of nanofibers (with diameters $\sim10$ nm) which are randomly oriented in the plane normal to the specific axis. |
Layered three-dimensional centrosymmetric crystals can exhibit characteristics of noncentrosymmetric materials. This happens when each individual layer alone lacks inversion, but, when combined, inversion symmetry is restored; hence the designation: locally noncentrosymmertic superconductors (LNCSs). |
We study the dynamic behaviour of a quantum two-level system with periodically varying parameters by solving the master equation for the density matrix. Two limiting cases are considered: multiphoton Rabi oscillations and Landau-Zener transitions. |
It is demonstrated that in the diffusive superconductor-ferromagnet-superconductor (S/F/S) junctions the current-phase relation is practically sinusoidal everywhere except in a narrow region near the 0-Pi transition. In this region the second harmonic dominates the scenario of the 0-Pi transition. |
Electromagnetic waves propagating in a layered superconductor with arbitrary momentum with respect to the main crystallographic directions display an unavoidable mixing between longitudinal and transverse degrees of freedom. Here we show that this basic physical mechanism explains the emergence of a well-defined absor... |
We report systematical studies of a new quasi-one-dimensional (1D) compound Ba3TiTe5 and the high-pressure induced superconductivity therein. Ba3TiTe5 was synthesized at high pressure and high temperature. |
Isothermal magnetic field dependence of magnetization and the magnetic relaxation measurements were performed for $H$$\parallel$c axis on single crystal of Ba(Fe$_{0.935}$Co$_{0.065}$)$_2$As$_2$ pnictide superconductor having $T_c$ = 21.7 K. The second magnetization peak (SMP) for each isothermal $M(H)$ was observed in... |
We describe here the properties expected of a higher (with emphasis on the order fourth) order phase transition. The order is identified in the sense first noted by Ehrenfest, namely in terms of the temperature dependence of the ordered state free energy near the phase boundary. |
We consider the shape of the curves of "Andreev" conductance of non-ballistic point contact NS heterosystems depending on the bias voltage at the contact. The obtained shape of those curves is caused by the contribution from the mechanism of coherent scattering by impurities which doubles the scattering cross ... |
We develop the formalism for computing the oscillations of the specific heat and thermal transport under rotated magnetic field in multiband superconductors with anisotropic gap and apply it to iron-pnictides. We show that these oscillations change sign at low temperatures and fields, which strongly influences the con... |
In the present work we study experimentally the influence that the domain structure of a fer- romagnet (FM) has on the properties of a superconductor (SC) in bilayers and multilayers of La0.60Ca0.40MnO3/Nb and FePt/Nb proximity hybrids. Specific experimental protocols that were employed in the performed magnetization ... |
We show that a microscopic theory of superfluidity, based on the properties of the many-body spectrum of a superfluid, can explain naturally the temperature dependence of critical velocities and the long time decay of supercurrents. |
Fe-clad MgB2 long tapes have been fabricated using a powder-in-tube technique. An Mg + 2B mixture was used as the central conductor core and reacted in-situ to form MgB2. |
In a d-wave superconductor with elastic impurity scattering, not all the available optical spectral weight goes into the condensate at zero temperature, and this leads to residual absorption. We find that for a range of impurity parameters in the intermediate coupling regime between Born (weak) and unitary (strong) li... |
A preformed-pair model was considered. The quantum disordered phase of the d-wave superconducting state was obtained by turning on an on-site repulsion. |
We derive the Ginzburg-Landau-Wilson theory for the superconducting phase transition in two dimensions and in the magnetic field. Without disorder the theory describes a fluctuation induced first-order quantum phase transition into the Abrikosov lattice. |
Magneto-transport measurements of Pr$_4$Ni$_3$O$_{10}$ single crystals performed under externally applied pressures up to 73 GPa in diamond anvil cells with either KBr or Nujol oil as pressure media yield signatures of superconductivity with a maximum onset temperature of approximately 31 K. True zero resistance was no... |
We report the synthesis, crystal structure, superconductivity and physical property characterizations of the ternary equiatomic compound ScRuSi. Polycrystalline samples of ScRuSi were prepared by an arc-melting method. |
We report the realization of grain alignment in Sn-added Sr1-xKxFe2As2 superconducting tapes prepared by ex-situ powder-in-tube method. At 4.2 K, high transport critical current densities Jc of 2.5x10^4 A/cm^2 (Ic = 180 A) in self-field and 3.5x10^3 A/cm^2 (Ic = 25.5 A) in 10 T have been measured. |
We consider superconductivity confined at a two-dimensional interface with a strong surface spin-orbit (Rashba) interaction. Some peculiar properties of this system are investigated. |
We propose to realize second-order topological superconductivity in bilayer spin-polarized Fermi gas superfluids. We focus on systems with intralayer chiral $p$-wave pairing and with tunable interlayer hopping and interlayer interactions. |
RuSr_2GdCu_2O_8 (Ru-1212) is a triple perovskite containing both CuO_2 and RuO_2 layers. It has attracted a great deal of interest recently because it displays electronic ferromagnetism and superconductivity coexisting on a microscopic scale, with T_Curie of 135K and T_c up to 50K. |
We report the first principle calculations of the lattice dynamics of KNi$_{2}$Se$_2$ together with the Raman scattering study. \ We have observed three out of four Raman active modes predicted by the factor group analysis. |
We have investigated the specific heat of optimally-doped iron chalcogenide superconductor Fe(Te0.57Se0.43) with a high-quality single crystal sample. The electronic specific heat Ce of this sample has been successfully separated from the phonon contribution using the specific heat of a non-superconducting sample (Fe0... |
Many-body systems, such as electrons flowing in a superconductor, are among the most difficult theoretical problems to study. A new family of exactly solvable models may offer some answers. |
In the quasi-two-dimensional (quasi-2D) copper- and iron-based superconductors, the onset of superconductivity is accompanied by a prominent peak in the magnetic spectrum at momenta close to the wave-vector of the nearby antiferromagnetic state. Such a peak is well described in terms of a spin resonance mode, i.e., a ... |
The search for topological superconductors and non-Abelian Majorana modes ranks among the most fascinating topics in condensed matter physics. There now exist several fundamental superconducting phases which host symmetry protected or chiral Majorana modes. |
From small-angle neutron scattering studies of the flux line lattice (FLL) in CeCoIn5, with magnetic field applied parallel to the crystal c-axis, we obtain the field- and temperature-dependence of the FLL form factor, which is a measure of the spatial variation of the field in the mixed state. We extend our earlier w... |
We show that an adiabatic increase of the supercurrent along a superconductor with lines of nodes of the order parameter on the Fermi surface can result in a cooling effect. The maximum cooling occurs if the supercurrent increases up to its critical value. |
Two simple bounds on the $T_c$ of conventional, phonon-mediated superconductors are derived within the framework of Eliashberg theory in the strong coupling regime. The first bound is set by the total electron-phonon coupling available within a material given the hypothetical ability to arbitrarily dope the material. |
Generalized BCS equations which consistently include the projection on the particle-number parity are derived from a systematic variational method. Numerical solutions are given that are illustrative of ultra-small metallic grains. |
We present electron-tunneling spectroscopy of oxygen over- and under-doped Bi-2212 single crystals in a temperature range between 14 K and 290 K using a break-junction technique. In over- and under-doped samples we observe a pseudogap with T* = 280 - 290 K and T* > 290 K, respectively. |
Single flux quantum (SFQ) based circuits are the subject of renewed attention due to their high speed and their very high energy efficiency. However, the need of cryogenic temperature, the complex physics of Josephson junctions and the lack of proper EDA tools causes slow progress in the field of superconducting elect... |
NiBi3 polycrystals were synthesized via a solid state method. X-ray diffraction analysis shows that the main phase present in the sample corresponds to NiBi3 in a weight fraction of 96.82 % according to the refinement of the crystalline structure. |
We examine the role of the anisotropy of superconducting critical thermal fluctuations in the opening of a pseudogap in a quasi-two dimensional superconductor such as a cuprate-oxide high-temperature superconductor. When the anisotropy between planes and their perpendicular axis is large enough and its superconducting... |
The bulk polycrystalline sample FeSe1/2Te1/2 is synthesized by solid state reaction route in an evacuated sealed quartz tube at 750 oC. The presence of superconductivity is confirmed through magnetization/thermoelectric/resistivity studies. |
We calculate the SIN and SIS tunneling conductances for the spin-fermion model. We argue that at strong spin-fermion coupling, relevant to cuprates, both conductances have dip features near the threshold frequencies when a tunneling electron begin emitting propagating spin excitation. |
We use scanning tunneling microscopy (STM) and quasiparticle interference (QPI) imaging to investigate the low-energy orbital texture of single-layer FeSe/SrTiO$_3$. We develop a $T$-matrix model of multi-orbital QPI to disentangle scattering intensities from Fe $3d_{xz}$ and $3d_{yz}$ bands, enabling the use of STM a... |
Delithiation of the known layered LiBC compound was predicted to induce conventional superconductivity at liquid nitrogen temperatures but extensive experimental work over the past two decades has detected no signs of the expected superconducting transition. Using a combination of first-principles stability analysis a... |
The nonlocal nature of unpaired Majorana bound states (MBSs) in topological superconductors can be exploited to create topologically protected qubits and perform gate operations fault-tolerantly via braidings. However, the time-dependent noises induced by coupling to an environment which is inevitable in any realistic... |
We report on an experimental and theoretical study of the high-frequency mixing properties of ion-irradiated YBa2Cu3O7 Josephson junctions embedded in THz antennas. We investigated the influence of the local oscillator power and frequency on the device performances. |
A band-projection formalism is developed for calculating the superfluid weight in two-dimensional multi-orbital superconductors with an orbital-dependent pairing. It is discovered that, in this case, the band geometric superfluid stiffness tensor can be locally non-positive-definite in some regions of the Brillouin zo... |
The O(oxygen)-M(metal)-O(oxygen) molecule is a basic unit of high-temperature superconducting cuprates and colossal magnetoresistance exhibiting manganates. This molecule can be regarded either as an element of a linear chain or as an ingredient of the corresponding cuprate or manganate lattice. |
We present the results of a microscopic calculation of the longitudinal thermal conductivity, $\kappa$, of a d-wave superconductor in the mixed state. Our results show an increase in the thermal conductivity with the applied field at low temperatures, and a decrease followed by a nearly field independent $\kappa(H)$ a... |
We have generated frequency combs spanning 0.5 to 20 GHz in superconducting half wave resonators at T=3 K. Thin films of niobium-titanium nitride enabled this development due to their low loss, high nonlinearity, low frequency dispersion, and high critical temperature. The combs nucleate as sidebands around multiples ... |
In this paper I study the energy resolved supercurrent of a junction consisting of a dirty normal metal between two superconductors. I also consider a cross geometry with two additional arms connecting the above mentioned junction with two normal reservoirs at equal and opposite voltages. |
Three-dimensional topological insulators (TIs) attract much attention due to its topologically protected Dirac surface states. Doping into TIs or their proximity with normal superconductors can promote the realization of topological superconductivity(SC) and Majorana fermions with potential applications in quantum com... |
The equations of viscous evolution of 3D arbitrarily shaped vortices in an isotropic type II superconductor and necessary boundary conditions are formulated in the frame of London approximation. The theory is applied to analyse characteristic scenaria of vortex penetration into current-carrying thick plate or bulk sam... |
The fundamental mechanism that gives rise to high-transition-temperature (high-Tc) superconductivity in the copper oxide materials has been debated since the discovery of the phenomenon. Recent work has focussed on a sharp 'kink' in the kinetic energy spectra of the electrons as a possible signature of the for... |
We formulate a quantitative theory of non-local electron transport in three-terminal disordered ferromagnet-superconductor-ferromagnet structures. We demonstrate that magnetic effects have different implications: While strong exchange field suppresses disorder-induced electron interference in ferromagnetic electrodes,... |
The interplay between novel topological states and superconductivity has garnered substantial interest due to its potential for topological quantum computing. The Josephson effect serves as a useful probe for edge superconductivity in these hybrid topological materials. |
Analysis of the a-b plane optical conductivity $\sigma_{ab}$ for both twinned and untwinned YBa$_{2}$Cu$_{3}$O$_{7-\delta}$ as a function of temperature and doping shows that below a well defined temperature T*, a dip in the spectrum systematically appears separating the infrared charge excitation spectrum into two com... |
A spin-triplet superconducting state mediated by ferromagnetic (FM) spin fluctuations has been suggested to occur in the newly discovered heavy-fermion superconductor UTe$_2$. However, the recent neutron scattering measurements revealed the presence of antiferromagnetic (AFM) spin fluctuations in UTe$_2$. |
Iron pnictides are the only known family of unconventional high-temperature superconductors besides cuprates. Until recently, it was widely accepted that superconductivity is spin-fluctuation driven and intimately related to their fermiology, specifically, hole and electron pockets separated by the same wave vector th... |
When magnetic field is applied parallel to the ab plane in d_{x^2-y^2}-wave superconductors, the transition of stable vortex lattice structure, spatial structure of local density of states, and specific heat oscillation by rotation of magnetic field orientation are investigated by quantitative calculations based on the... |
In this paper we provide a comprehesive analysis of different properties of pnictides both in the normal and superconducting state, with a particular focus on the optimally-doped Ba$_{1-x}$K$_{x}$Fe$_2$As$_2$ system. We show that, by using the band dispersions experimentally measured by ARPES, a four-band Eliashberg m... |
The recent discovery of intermediate-temperature superconductivity (ITC) in MgB2 by Akimitsu et al. and its almost simultaneous explanation in terms of a hole-carrier-based pairing mechanism by Hirsch, has triggered an avalanche of studies of its structural, magnetic and transport properties. As a further contribution... |
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