Stefano Martiniani

New York University | NYU · Department of Physics

We propose an efficient Monte Carlo method for the computation of the volumes of high-dimensional bodies with arbitrary shape. We start with a region of known volume within the interior of the manifold and then use the multi-state Bennett acceptance-ratio method to compute the dimensionless free-energy difference between a series of equilibrium sim...

In the late 1980s, Sam Edwards proposed a possible statistical-mechanical framework to describe the properties of disordered granular materials. A key assumption underlying the theory was that all jammed packings are equally likely. In the intervening years it has never been possible to test this bold hypothesis directly. Here we present simulation...

While the equilibrium properties, states, and phase transitions of interacting systems are well described by statistical mechanics, the lack of suitable state parameters has hindered the understanding of non-equilibrium phenomena in diverse settings, from glasses to driven systems to biology. The length of a losslessly compressed data file is a dir...

Time-reversal symmetry breaking and entropy production are universal features of nonequilibrium phenomena. Despite its importance in the physics of active and living systems, the entropy production of systems with many degrees of freedom has remained of little practical significance because the high-dimensionality of their state space makes it diff...

Computable information density (CID), the ratio of the length of a losslessly compressed data file to that of the uncompressed file, is a measure of order and correlation in both equilibrium and nonequilibrium systems. Here we show that correlation lengths can be obtained by decimation, thinning a configuration by sampling data at increasing interv...

Randomly moving active particles can be herded into directed motion by asymmetric geometric structures. Although such a rectification process has been extensively studied due to its fundamental, biological, and technological relevance, a comprehensive understanding of active matter rectification based on single particle dynamics remains elusive. He...

Stochastic gradient descent (SGD) is a fundamental tool for training deep neural networks across a variety of tasks. In self-supervised learning, different input categories map to distinct manifolds in the embedded neural state space. Accurate classification is achieved by separating these manifolds during learning, akin to a packing problem. We in...

We introduce a new class of functional correlated disordered materials, termed Gyromorphs, which uniquely combine liquid-like translational disorder with quasi-long-range rotational order, induced by a ring of $G$ delta peaks in their structure factor. We generate gyromorphs in $2d$ and $3d$ by spectral optimization methods, verifying that they dis...

Stability in recurrent neural models poses a significant challenge, particularly in developing biologically plausible neurodynamical models that can be seamlessly trained. Traditional cortical circuit models are notoriously difficult to train due to expansive nonlinearities in the dynamical system, leading to an optimization problem with nonlinear...

Stability in recurrent neural models poses a significant challenge, particularly in developing biologically plausible neurodynamical models that can be seamlessly trained. Traditional cortical circuit models are notoriously difficult to train due to expansive nonlinearities in the dynamical system, leading to an optimization problem with nonlinear...

The energy landscape is central to understanding low-temperature and athermal systems, like jammed soft spheres. The geometry of this high-dimensional energy surface is controlled by a plethora of minima and their associated basins of attraction that escape analytical treatment and are thus studied numerically. We show that the ODE solver with the...

Media with correlated disorder display unexpected transport properties, but it is still a challenge to design structures with desired spectral features at scale. In this work, we introduce an optimal formulation of this inverse problem by means of the nonuniform fast Fourier transform, thus arriving at an algorithm capable of generating systems wit...

We present a geometric design rule for size-controlled clustering of self-propelled particles. Active particles that tend to rotate under an external force have an intrinsic signed-parameter with units of curvature, which we term curvity, derivable from first principles. Robot experiments and numerical simulations show that the properties of the in...

A force field as accurate as quantum mechanics (QM) and as fast as molecular mechanics (MM), with which one can simulate a biomolecular system efficiently enough and meaningfully enough to get quantitative insights, is among the most ardent dreams of biophysicists -- a dream, nevertheless, not to be fulfilled any time soon. Machine learning force f...

Stochasticity plays a central role in nearly every biological process, and the noise power spectral density (PSD) is a critical tool for understanding variability and information processing in living systems. In steady state, many such processes can be described by stochastic linear time-invariant (LTI) systems driven by Gaussian white noise, whose...

Data-driven interatomic potentials (IPs) trained on large collections of first principles calculations are rapidly becoming essential tools in the fields of computational materials science and chemistry for performing atomic-scale simulations. Despite this, apart from a few notable exceptions, there is a distinct lack of well-organized, public data...

Engineered proteins have emerged as novel diagnostics, therapeutics, and catalysts. Often, poor protein developability─quantified by expression, solubility, and stability─hinders utility. The ability to predict protein developability from amino acid sequence would reduce the experimental burden when selecting candidates. Recent advances in screenin...

Randomly moving active particles can be herded into directed motion by asymmetric geometric structures. Although such a rectification process has been extensively studied due to its fundamental, biological, and technological relevance, a comprehensive understanding of active matter rectification based on single particle dynamics remains elusive. He...

Data-driven (DD) interatomic potentials (IPs) trained on large collections of first principles calculations are rapidly becoming essential tools in the fields of computational materials science and chemistry for performing atomic-scale simulations. Despite this, apart from a few notable exceptions, there is a distinct lack of well-organized, public...

Stochasticity plays a central role in nearly every biological process, and the noise power spectral density (PSD) is a critical tool for understanding variability and information processing in living systems. In steady-state, many such processes can be described by stochastic linear time-invariant (LTI) systems driven by Gaussian white noise, whose...

Media with correlated disorder have recently garnered a lot of attention for their unexpected transport properties. A critical first step towards understanding their complex structure-function relationship is to devise methods for designing structures with desired spectral features at scale. In this work, we introduce an optimal formulation of this...

The brain relies on communication between specialized cortical areas to accomplish complex cognitive tasks. To understand this ability of the brain, we need a deeper understanding of information transfer across cortical areas. There are two leading hypotheses for communication between cortical areas: 1) The communication through coherence (CTC) hyp...

In statistical mechanics, measuring the number of available states and their probabilities, and thus the system’s entropy, enables the prediction of the macroscopic properties of a physical system at equilibrium. This predictive capacity hinges on the knowledge of the a priori probabilities of observing the states of the system, given by the Boltzm...

We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of hard spheres in $d=3$ dimensions, and thus obtain an estimate of the random close packing (RCP) volume fraction,...

We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of hard spheres in $d=3$ dimensions, and thus obtain an estimate of the random close packing (RCP) volume fraction,...

Engineered proteins have emerged as novel diagnostics, therapeutics, and catalysts. Often, poor protein developability – quantified by expression, solubility, and stability – hinders utility. The ability to predict protein developability from amino acid sequence would reduce the experimental burden when selecting candidates. Recent advances in scre...

Time-reversal symmetry breaking and entropy production are universal features of nonequilibrium phenomena. Despite its importance in the physics of active and living systems, the entropy production of systems with many degrees of freedom has remained of little practical significance because the high dimensionality of their state space makes it diff...

In statistical mechanics, measuring the number of available states and their probabilities, and thus the system's entropy, enables the prediction of the macroscopic properties of a physical system at equilibrium. This predictive capacity hinges on the knowledge of the a priori probabilities of observing the states of the system, given by the Boltzm...

Collective behavior, both in real biological systems and in theoretical models, often displays a rich combination of different kinds of order. A clear-cut and unique definition of “phase” based on the standard concept of the order parameter may therefore be complicated, and made even trickier by the lack of thermodynamic equilibrium. Compression-ba...

Significance Poor protein developability is a critical hindrance to biologic discovery and engineering. Experimental capacity limits variant analysis. We demonstrate the ability of an on-yeast protease assay, a split green fluorescent protein assay, and a split β-lactamase assay to predict recombinant protein production yields in bacteria. The assa...

Proteins require high developability - quantified by expression, solubility, and stability - for robust utility as therapeutics, diagnostics, and in other biotechnological applications. Measuring traditional developability metrics is low-throughput in nature, often slowing the developmental pipeline. We evaluated the ability of three high-throughpu...

Collective behavior, both in real biological systems as well as in theoretical models, often displays a rich combination of different kinds of order. A clear-cut and unique definition of "phase" based on the standard concept of order parameter may therefore be complicated, and made even trickier by the lack of thermodynamic equilibrium. Compression...

Computable Information Density (CID), the ratio of the length of a losslessly compressed data file to that of the uncompressed file, is a measure of order and correlation in both equilibrium and nonequilibrium systems. Here we show that correlation lengths can be obtained by decimation - thinning a configuration by sampling data at increasing inter...

While the equilibrium properties, states, and phase transitions of interacting systems are well described by statistical mechanics, the lack of suitable state parameters has hindered the understanding of non-equilibrium phenomena in diverse settings, from glasses to driven systems to biology. The length of a losslessly compressed data file is a dir...

Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can b...

When the states of a system can be described by the extrema of a high-dimensional function, the characterisation of its complexity, i.e. the enumeration of the accessible stable states, can be reduced to a sampling problem. In this thesis a robust numerical protocol is established, capable of producing numerical estimates of the total number of sta...

Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can b...

Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can b...

Significance Markov chain Monte Carlo is the method of choice for sampling high-dimensional (parameter) spaces. The method requires knowledge of the weight function (or likelihood function) determining the probability that a state is observed. However, in many numerical applications the weight function itself is fluctuating. Here, we present an app...

Conventional Monte Carlo simulations are stochastic in the sense that the acceptance of a trial move is decided by comparing a computed acceptance probability with a random number, uniformly distributed between 0 and 1. Here we consider the case that the weight determining the acceptance probability itself is fluctuating. This situation is common i...

In the late 1980s, Sir Sam Edwards proposed a possible statistical-mechanical framework to describe the properties of disordered granular materials. A key assumption underlying the theory was that all jammed packings are equally likely. In the intervening years it has never been possible to test this bold hypothesis directly. Here we present simula...

We propose an efficient Monte Carlo method for the computation of the volumes of high-dimensional bodies with arbitrary shape. We start with a region of known volume within the interior of the manifold and then use the multistate Bennett acceptance-ratio method to compute the dimensionless free-energy difference between a series of equilibrium simu...

We propose an efficient Monte Carlo method for the computation of the volumes of high-dimensional bodies with arbitrary shape. We start with a region of known volume within the interior of the manifold and then use the multistate Bennett acceptance-ratio method to compute the dimensionless free-energy difference between a series of equilibrium simu...

We report a numerical calculation of the total number of disordered jammed configurations $\Omega$ of $N$ repulsive, three-dimensional spheres in a fixed volume $V$. To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. (Phys. Rev. Lett. 106, 245502 (2011)) and Asenjo et al. (Phys. Rev. Lett. 11...

We review a number of recently developed strategies for enhanced sampling of complex systems based on knowledge of the potential energy landscape. We describe four approaches, replica exchange, Kirkwood sampling, superposition‐enhanced nested sampling, and basin sampling, and show how each of them can exploit information for low‐lying potential ene...

The theoretical analysis of many problems in physics, astronomy and applied mathematics requires an efficient numerical exploration of multimodal parameter spaces that exhibit broken ergodicity. Monte Carlo methods are widely used to deal with these classes of problems, but such simulations suffer from a ubiquitous sampling problem: the probability...

A NIR absorbing squaraine dye has been synthesized as a sensitizer for use in dye-sensitized solar cells (DSCs). Following computational calculations, a benz[cd]indole moiety was selected as an electron-rich heterocyclic component and condensed with indole-based emisquaraine bearing a carboxyl group, as an anchor for their immobilization on TiO2, t...

Electron transfer from TiO2 to iodine/iodide electrolytes proceeds via reduction of either I3– or uncomplexed I2 (free iodine), but which route predominates has not previously been determined. By measurement of the electron lifetime while independently varying free iodine or I3– concentrations, we find the lifetime is correlated with free-iodine co...

The order of regeneration for DSCs based on two organic dyes has been investigated by transient absorption spectroscopy on devices under operating conditions and determined to be 2nd order in iodide. The results shed light on the mechanism and limits to the regeneration rate relative to oxidation potential.