Article
Physics, Multidisciplinary
Qianyi Li, Haim Sompolinsky
Summary: This study examines the statistical mechanics of learning in deep linear neural networks, shedding light on their nonlinear learning properties and essential network characteristics such as generalization error, network width and depth, and training set size. By introducing backpropagating kernel renormalization and incremental integration of weights layer by layer, important network properties are accurately evaluated, offering insights into the emergent properties of neural representations across hidden layers.
Article
Physics, Multidisciplinary
Claudia Loyola, Sergio Davis, Joaquin Peralta
Summary: Homogeneous and highly inhomogeneous melting of crystals have been studied. Evidence of metastable solid phase produced from nonequilibrium initial condition was obtained through molecular dynamics simulations, which is important for understanding highly inhomogeneous melting phenomena.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Physics, Multidisciplinary
A. N. Pearson, Y. Guryanova, P. Erker, E. A. Laird, G. A. D. Briggs, M. Huber, N. Ares
Summary: Research demonstrates that there is a linear relationship between the accuracy of clocks and entropy, with experimental measurements showing this relationship exists in nanoscale clocks and operates within an order of magnitude of the theoretical limit.
Article
Physics, Fluids & Plasmas
Soumen Das, Shankar Ghosh, Shamik Gupta
Summary: This paper discusses the dynamics of rigid objects and proposes a coarse-grained modeling approach by treating it as a Markov process, effectively reducing the dimensionality of the configuration space.
Article
Physics, Multidisciplinary
M. Buchhold, Y. Minoguchi, A. Altland, S. Diehl
Summary: The study investigates the state updates of a wave function under time evolution and measurements, identifying a competition between different elements of dynamics. By constructing an n-replica Keldysh field theory, the decoupling of degrees of freedom is found to be exact for free theories, providing insights into the behavior of interacting theories.
Article
Physics, Multidisciplinary
Matthieu Barbier, Claire de Mazancourt, Michel Loreau, Guy Bunin
Summary: The study finds that in an ecological system, species interactions are highly disordered while exhibiting a diffuse statistical structure: successful competitors subtly favor each other and partition their impacts on other species. This pattern is strongly supported by empirical evidence from grassland biodiversity experiments.
Article
Physics, Multidisciplinary
T. Mendes-Santos, X. Turkeshi, M. Dalmonte, Alex Rodriguez
Summary: The study focuses on the intrinsic dimension of data sets near phase transitions, finding that it uniquely characterizes the transition regime in various cases. Finite-size analysis allows for accurate identification of critical points and determination of critical exponents, overcoming limitations of other unsupervised learning methods. The work reveals unique signatures of universal behavior in raw data sets and suggests a direct parallelism between conventional order parameters and intrinsic dimension.
Article
Physics, Multidisciplinary
Stephen Whitelam
Summary: We utilize Monte Carlo and genetic algorithms to train neural-network feedback-control protocols in order to convert measurement information into stored work or heat in fluctuating nanosystems. These protocols are capable of extracting work from a colloidal particle pulled by an optical trap and absorbing entropy by an Ising model undergoing magnetization reversal. The learning framework does not require prior knowledge of the system, only relies on experimentally accessible measurements, and can be scaled to complex systems.
Article
Physics, Fluids & Plasmas
Ignacio S. Gomez
Summary: We study a generalization of the random walk (RW) based on a deformed translation of the unitary step, inherited by the q algebra, a mathematical structure underlying nonextensive statistics. The RW with deformed step implies an associated deformed random walk (DRW) provided with a deformed Pascal triangle along with an inhomogeneous diffusion. The paths of the RW in deformed space are divergent, while those corresponding to the DRW converge to a fixed point.
Article
Chemistry, Physical
Dibyajyoti Mohanta, Debaprasad Giri, Sanjay Kumar
Summary: The equilibrium properties of double stranded DNA (dsDNA) on an attractive surface were studied using the self avoiding walk (SAW) model. The study observed simultaneous adsorption and force induced melting transitions, and investigated different phases of DNA. It was found that melting is primarily influenced by entropy and can be reduced under the application of a force. Different scenarios of surface attraction were considered, and it was observed that a strongly attractive surface resulted in adsorption-induced unzipping of the DNA.
Article
Physics, Fluids & Plasmas
Rytis Kazakevicius, Aleksejus Kononovicius
Summary: This paper examines the behavior of voter models in terms of anomalous diffusion, showing that the original model exhibits a ballistic regime. Through numerical simulations and analytical approximations, the study reveals different diffusion regimes and confirms the temporal evolution of the raw moments.
Article
Physics, Multidisciplinary
Efe Ilker, Ozenc Gungor, Benjamin Kuznets-Speck, Joshua Chiel, Sebastian Deffner, Michael Hinczewski
Summary: Biochemical reaction networks regulating living systems are stochastic, and the use of counterdiabatic driving can control biological processes, with the possibility of implementing local control to adapt to limited external control in biological systems.
Article
Physics, Multidisciplinary
Jannes Gladrow, Ulrich F. Keyser, R. Adhikari, Julian Kappler
Summary: This study establishes a protocol for extracting ratios of path probabilities from measured time series, bridging the gap between theory and experiment. By conducting experiments on a single colloidal particle in a microchannel, both ratios of path probabilities and the most probable path for a barrier crossing were successfully extracted, showing excellent agreement with independently calculated predictions. The experimental results at room temperature were found to be inconsistent with the low-noise Freidlin-Wentzell stochastic action, while the experimentally accessible ratio of path probabilities is uniquely determined.
Article
Physics, Multidisciplinary
R. Finkelstein, O. Lahad, I Cohen, O. Davidson, S. Kiriati, E. Poem, O. Firstenberg
Summary: A scheme is introduced to eliminate the inhomogeneous dephasing of a collective quantum state by continuously dressing the collective state with an auxiliary sensor state using off-resonant fields. The scheme is experimentally demonstrated to completely suppress inhomogeneous dephasing and prolong memory time. It can be applied to improve the performance of quantum gates and memories with neutral atoms in various systems.
Article
Astronomy & Astrophysics
Yidian Chen, Danning Li, Mei Huang
Summary: In this study, we investigate inhomogeneous chiral condensation under rotation considering finite size effects and boundary conditions in the holographic QCD model. We find that the effect of finite size on condensation depends on the boundary conditions, and the temperature and angular velocity significantly affect the phase diagrams of QCD.
Article
Biophysics
Marc Joyeux
BIOPHYSICAL JOURNAL
(2020)
Article
Physics, Condensed Matter
Jalal Sarabadani, Sahin Buyukdagli, Tapio Ala-Nissila
JOURNAL OF PHYSICS-CONDENSED MATTER
(2020)
Article
Biophysics
Marc Joyeux, Ivan Junier
BIOPHYSICAL JOURNAL
(2020)
Article
Biophysics
Marc Joyeux
Summary: This study investigates the impact of self-association of nucleoid proteins on their architectural properties, demonstrating that self-association greatly enhances their ability to shape the DNA coil. Different forms of self-association lead to significant changes in the organization of the DNA coil.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Physical
Sahin Buyukdagli
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
Sahin Buyukdagli, Rudolf Podgornik
Summary: The study investigates the interactions of zwitterionic membranes with rotating surface dipoles immersed in monovalent salt. It reveals a non-uniform trend in the electrostatic forces between membranes at different distances, indicating significant implications for membrane adhesion and separation techniques.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Sahin Buyukdagli
Summary: Membrane engineering techniques, such as carbon nanotube coating, can alter the properties of dielectric membranes and enable new molecular transport strategies. By manipulating polymer translocation dynamics in dielectric membrane pores using multivalent ions, an efficient means of driving overall neutral or weakly charged analytes can be achieved, boosting resolution in nanopore-based biosensing techniques.
Article
Chemistry, Physical
Marc Joyeux
Summary: This study developed a coarse-grained model to simulate the interplay between DNA supercoiling, topological barriers, and molecular motors. The results showed that the positions of topological barriers and molecular motors have an influence on the helical structure and steady state values of DNA. This model can support experimental efforts and help decipher the organizational mechanisms of bacterial chromosomes.
MOLECULAR SIMULATION
(2022)
Article
Microbiology
Marc Joyeux
Summary: The genomic DNA of bacteria, called the nucleoid, is compacted through the cross-linking of DNA by nucleoid proteins and the separation of DNA and other macromolecules. This study investigates the interplay between DNA-bridging proteins and globular macromolecular crowders in organizing the nucleoid. Simulations show that the radius of gyration of the DNA coil decreases with the volume ratio of globular crowders and the number of DNA bridges formed by nucleoid proteins. Non-associating proteins contribute to nucleoid compaction while maintaining high mobility, while self-associating proteins form a deformable network that cross-links the DNA chain.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Physics, Fluids & Plasmas
Sahin Buyukdagli
Summary: From a field-theoretic partition function of an electrolyte confined between two anionic membranes, a contact-value identity is derived, which is valid for general intramolecular solute structure and electrostatic coupling strength. The inner charge spread of the solute particles is shown to induce the twofold enhancement of the short-range membrane repulsion and a longer-range depletion attraction. The inclusion of dielectric contrast between the electrolyte and interacting membranes amplifies the solute specificity of macromolecular interactions.
Article
Physics, Fluids & Plasmas
Xiang Yang, Sahin Buyukdagli, Alberto Scacchi, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: EP mobility reversal refers to the phenomenon where the direction of polymer drift driven by an external electric field is reversed due to the change in sign of the counterion-dressed surface charge. In order to understand this counterintuitive effect, a strong-coupling-dressed Poisson-Boltzmann approach is applied to the cylindrical geometry of the polyelectrolyte-salt system. The derived analytical polymer mobility formula predicts that the increment of monovalent salt, the decrease of multivalent counterion valency, and the increase of the dielectric permittivity of the solvent suppress charge correlations and increase the concentration of multivalent bulk counterions required for EP mobility reversal. Coarse-grained molecular dynamics simulations support these predictions and show the induction of mobility inversion by multivalent counterions at dilute concentrations.
Article
Physics, Multidisciplinary
Sahin Buyukdagli
Summary: In this article, the signatures of translocating polymers in magnetic fields induced by ionic currents were investigated. It was found that the translocating polymer suppresses the induced magnetic field in voltage-driven transport, while the magnetic field reduction in pressure-driven transport is caused by the negative electrokinetic contribution of anionic DNA surface charges. The integration of magnetic field detection techniques into current biosequencing approaches can efficiently complement conventional biosensing strategies with high susceptibility to background noise.
TURKISH JOURNAL OF PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Sahin Buyukdagli
Summary: The DLVO theory is highly accurate for characterizing macromolecular stability in water solvent, but the reason behind its accuracy is puzzling. Through research, it has been found that for hydrophobic membranes with fixed charges embedded in the surface, the various explicit solvent effects are nearly canceled out, keeping the intermembrane pressure close to the double-layer force of the DLVO theory. For hydrophilic surface charge groups within the aqueous region, the solvent molecules' influence on the membrane interaction force is suppressed by the hydration of the lipid head groups.
Article
Chemistry, Physical
Sahin Buyukdagli
Summary: In this study, we propose an electrolyte model composed of solvent molecules and salt ions, and investigate the salt-induced dielectric decrement by considering salt-solvent correlations. By using a virial expansion to treat the salt charges, we are able to explicitly include the many-body salt-solvent interactions and explain the experimentally observed linear decay of electrolyte permittivity with added dilute salt. Our findings indicate that the reduction of solvent permittivity is caused by the salt screening of polarization charges, which suppresses the dielectric response of the solvent. We also demonstrate that our model can accurately reproduce various experimental trends, such as the attenuation of electrolyte permittivity with rising temperature and its intensification with salt valency.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Sahin Buyukdagli, Rudolf Podgornik