arXiv subjects

Artemy Kolchinsky

Publications and source records attributed to Artemy Kolchinsky.

At least 37 records · Page 2Linked to original sources

arXiv2024

Thermodynamic dissipation does not bound replicator growth and decay rates

In a well-known paper, Jeremy England derived a bound on the free energy dissipated by a self-replicating system [England, "Statistical physics of self-replication", The Journal of Chemical Physics, 2013]. This bound is usually interpreted as a universal relationship that connects thermodynamic dissipation to replicator per-capita decay and growth rates. We argue from basic thermodynamic principles against this interpretation. In fact, we suggest that such a relationship cannot exist in principle, because it is impossible for a thermodynamically-consistent replicator to undergo both per-capita growth and per-capita decay back into reactants. Instead, replicator may decay into separate waste products, but in that case, replication and decay are two independent physical processes, and there is no universal relationship that connects their thermodynamic and dynamical properties.

cond-mat.stat-mech↗

arXiv2024

Partial information decomposition: redundancy as information bottleneck

The partial information decomposition (PID) aims to quantify the amount of redundant information that a set of sources provides about a target. Here, we show that this goal can be formulated as a type of information bottleneck (IB) problem, termed the "redundancy bottleneck" (RB). The RB formalizes a tradeoff between prediction and compression: it extracts information from the sources that best predict the target, without revealing which source provided the information. It can be understood as a generalization of "Blackwell redundancy", which we previously proposed as a principled measure of PID redundancy. The "RB curve" quantifies the prediction--compression tradeoff at multiple scales. This curve can also be quantified for individual sources, allowing subsets of redundant sources to be identified without combinatorial optimization. We provide an efficient iterative algorithm for computing the RB curve.

cs.IT↗

arXiv2024

Metabolism, information, and viability in a simulated physically-plausible protocell

Critical experimental design issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer (a ruthenium complex) to turn resource molecules into building blocks, in a manner that is modulated by a combinatorial DNA-based co-factor. This co-factor molecule serves as part of an electron relay for the energy transduction mechanism, where the charge-transport rates depend on the sequence that contains an oxo-guanine. The co-factor also acts as a store of inheritable information due to its ability to replicate non-enzymatically through template-directed ligation. Together, the energy transducer and the co-factor act as a metabolic catalyst that produces co-factor DNA building blocks as well as fatty acids (from picolinium ester and modified DNA oligomers), where the fatty acids self-assemble into vesicles on which exterior surface both the co-factor (DNA) and the energy transducer are anchored with hydrophobic tails. Here we use simulations to study how the co-factor sequence determines its fitness as reflected by charge transfer and replication rates. To estimate the impact on the protocell, we compare these rates with previously measured metabolic rates from a similar system where the charge transfer is directly between the ruthenium complex and the oxo-guanine (without DNA replication and charge transport). Replication and charge transport turn out to have different and often opposing sequence requirements. Functional information of the co-factor molecules is used to probe the feasibility of randomly picking co-factor sequences from a limited population of co-factors molecules, where a good co-factor can enhance both metabolic biomass production and its own replication rate.

physics.bio-ph↗

arXiv2024

Universal bounds on optimization of free energy harvesting

Harvesting free energy from the environment is essential for the operation of many biological and artificial systems. We investigate the maximum rate of harvesting achievable by optimizing a set of reactions in a Markovian system, possibly given topological, kinetic, and thermodynamic constraints. We show that the maximum harvesting rate can be expressed as a variational principle, which we solve in closed-form for three physically meaningful regimes. Our approach is relevant for optimal design and for quantifying efficiency of existing reactions. Our results are illustrated on bacteriorhodopsin, a light-driven proton pump from Archae, which is found to be close to optimal under realistic conditions.

cond-mat.stat-mech↗

arXiv2024

Thermodynamic bounds on spectral perturbations, with applications to oscillations and relaxation dynamics

In discrete-state Markovian systems, many important properties of correlations functions and relaxation dynamics depend on the spectrum of the rate matrix. Here we demonstrate the existence of a universal trade-off between thermodynamic and spectral properties. We show that the entropy production rate, the fundamental thermodynamic cost of a nonequilibrium steady state, bounds the difference between the eigenvalues of a nonequilibrium rate matrix and a reference equilibrium rate matrix. Using this result, we derive thermodynamic bounds on the spectral gap, which governs autocorrelations times and the speed of relaxation to steady state. We also derive thermodynamic bounds on the imaginary eigenvalues, which govern the speed of oscillations. We illustrate our approach using a simple model of biomolecular sensing.

cond-mat.stat-mech↗

arXiv2023

Semantic Information in a model of Resource Gathering Agents

We explore the application of a new theory of Semantic Information to the well-motivated problem of a resource foraging agent. Semantic information is defined as the subset of correlations, measured via the transfer entropy, between agent $A$ and environment $E$ that is necessary for the agent to maintain its viability $V$. Viability, in turn, is endogenously defined as opposed to the use of exogenous quantities like utility functions. In our model, the forager's movements are determined by its ability to measure, via a sensor, the presence of an individual unit of resource, while the viability function is its expected lifetime. Through counterfactual interventions -- scrambling the correlations between agent and environment via noising the sensor -- we demonstrate the presence of a critical value of the noise parameter, $η_c$, above which the forager's expected lifetime is dramatically reduced. On the other hand, for $η< η_c$ there is little-to-no effect on its ability to survive. We refer to this boundary as the semantic threshold, quantifying the subset of agent-environment correlations that the agent actually needs to maintain its desired state of staying alive. Each bit of information affects the agent's ability to persist both above and below the semantic threshold. Modeling the viability curve and its semantic threshold via forager/environment parameters, we show how the correlations are instantiated. Our work provides a useful model for studies of established agents in terms of semantic information. It also shows that such semantic thresholds may prove useful for understanding the role information plays in allowing systems to become autonomous agents.

cond-mat.stat-mech↗

arXiv2023

What it takes to solve the Origin(s) of Life: An integrated review of techniques

Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number of different scientific perspectives relevant to the problem has resulted in the coexistence of diverse tools, techniques, data, and software in OoL studies. This has made communication between the disciplines relevant to the OoL extremely difficult because the interpretation of data, analyses, or standards of evidence can vary dramatically. Here, we hope to bridge this wide field of study by providing common ground via the consolidation of tools and techniques rather than positing a unifying view on how life emerges. We review the common tools and techniques that have been used significantly in OoL studies in recent years. In particular, we aim to identify which information is most relevant for comparing and integrating the results of experimental analyses into mathematical and computational models. This review aims to provide a baseline expectation and understanding of technical aspects of origins research, rather than being a primer on any particular topic. As such, it spans broadly -- from analytical chemistry to mathematical models -- and highlights areas of future work that will benefit from a multidisciplinary approach to tackling the mystery of life's origin. Ultimately, we hope to empower a new generation of OoL scientists by reviewing how they can investigate life's origin, rather than dictating how to think about the problem.

q-bio.PE↗

arXiv2023

Thermodynamic Bound on the Asymmetry of Cross-Correlations

The principle of microscopic reversibility says that, in equilibrium, two-time cross-correlations are symmetric under the exchange of observables. Thus, the asymmetry of cross-correlations is a fundamental, measurable, and often-used statistical signature of deviation from equilibrium. Here we find a simple and universal inequality that bounds the magnitude of asymmetry by the cycle affinity, i.e., the strength of thermodynamic driving. Our result applies to a large class of systems and all state observables, and it suggests a fundamental thermodynamic cost for various nonequilibrium functions quantified by the asymmetry. It also provides a powerful tool to infer affinity from measured cross-correlations, in a different and complementary way to the thermodynamic uncertainty relations. As an application, we prove a thermodynamic bound on the coherence of noisy oscillations, which was previously conjectured by Barato and Seifert [Phys. Rev. E 95, 062409 (2017)]. We also derive a thermodynamic bound on directed information flow in a biochemical signal transduction model.

cond-mat.stat-mech↗

arXiv2023

Thermodynamics of computing with circuits

Digital computers implement computations using circuits, as do many naturally occurring systems (e.g., gene regulatory networks). The topology of any such circuit restricts which variables may be physically coupled during the operation of a circuit. We investigate how such restrictions on the physical coupling affects the thermodynamic costs of running the circuit. To do this we first calculate the minimal additional entropy production that arises when we run a given gate in a circuit. We then build on this calculation, to analyze how the thermodynamic costs of implementing a computation with a full circuit, comprising multiple connected gates, depends on the topology of that circuit. This analysis provides a rich new set of optimization problems that must be addressed by any designer of a circuit, if they wish to minimize thermodynamic costs.

cond-mat.stat-mech↗

arXiv2023

Thermodynamically ideal quantum-state inputs to any device

We investigate and ascertain the ideal inputs to any finite-time thermodynamic process. We demonstrate that the expectation values of entropy flow, heat, and work can all be determined via Hermitian observables of the initial state. These Hermitian operators encapsulate the breadth of behavior and the ideal inputs for common thermodynamic objectives. We show how to construct these Hermitian operators from measurements of thermodynamic output from a finite number of effectively arbitrary inputs. Behavior of a small number of test inputs thus determines the full range of thermodynamic behavior from all inputs. For any process, entropy flow, heat, and work can all be extremized by pure input states -- eigenstates of the respective operators. In contrast, the input states that minimize entropy production or maximize the change in free energy are non-pure mixed states obtained from the operators as the solution of a convex optimization problem. To attain these, we provide an easily implementable gradient descent method on the manifold of density matrices, where an analytic solution yields a valid direction of descent at each iterative step. Ideal inputs within a limited domain, and their associated thermodynamic operators, are obtained with less effort. This allows analysis of ideal thermodynamic inputs within quantum subspaces of infinite-dimensional quantum systems; it also allows analysis of ideal inputs in the classical limit. Our examples illustrate the diversity of 'ideal' inputs: Distinct initial states minimize entropy production, extremize the change in free energy, and maximize work extraction.

quant-ph↗

arXiv2023

Housekeeping and excess entropy production for general nonlinear dynamics

We propose a housekeeping/excess decomposition of entropy production for general nonlinear dynamics in a discrete space, including chemical reaction networks and discrete stochastic systems. We exploit the geometric structure of thermodynamic forces to define the decomposition; this does not rely on the notion of a steady state, and even applies to systems that exhibit multistability, limit cycles, and chaos. In the decomposition, distinct aspects of the dynamics contribute separately to entropy production: the housekeeping part stems from a cyclic mode that arises from external driving, generalizing Schnakenberg's cyclic decomposition to non-steady states, while the excess part stems from an instantaneous relaxation mode that arises from conservative forces. Our decomposition refines previously known thermodynamic uncertainty relations and speed limits. In particular, it not only improves an optimal-transport-theoretic speed limit, but also extends the optimal transport theory of discrete systems to nonlinear and nonconservative settings.

cond-mat.stat-mech↗

arXiv2022

Information geometry of excess and housekeeping entropy production

A nonequilibrium system is characterized by a set of thermodynamic forces and fluxes which give rise to entropy production (EP). We show that these forces and fluxes have an information-geometric structure, which allows us to decompose EP into contributions from different types of forces in general (linear and nonlinear) discrete systems. We focus on the excess and housekeeping decomposition, which separates contributions from conservative and nonconservative forces. Unlike the Hatano-Sasa decomposition, our housekeeping/excess terms are always well-defined, including in systems with odd variables and nonlinear systems without steady states. Our decomposition leads to far-from-equilibrium thermodynamic uncertainty relations and speed limits. As an illustration, we derive a thermodynamic bound on the time necessary for one cycle in a chemical oscillator.

cond-mat.stat-mech↗

arXiv2022

The Computational Capacity of LRC, Memristive and Hybrid Reservoirs

Reservoir computing is a machine learning paradigm that uses a high-dimensional dynamical system, or \emph{reservoir}, to approximate and predict time series data. The scale, speed and power usage of reservoir computers could be enhanced by constructing reservoirs out of electronic circuits, and several experimental studies have demonstrated promise in this direction. However, designing quality reservoirs requires a precise understanding of how such circuits process and store information. We analyze the feasibility and optimal design of electronic reservoirs that include both linear elements (resistors, inductors, and capacitors) and nonlinear memory elements called memristors. We provide analytic results regarding the feasibility of these reservoirs, and give a systematic characterization of their computational properties by examining the types of input-output relationships that they can approximate. This allows us to design reservoirs with optimal properties. By introducing measures of the total linear and nonlinear computational capacities of the reservoir, we are able to design electronic circuits whose total computational capacity scales extensively with the system size. Our electronic reservoirs can match or exceed the performance of conventional "echo state network" reservoirs in a form that may be directly implemented in hardware.

cs.NE↗

arXiv2022

Dependence of integrated, instantaneous, and fluctuating entropy production on the initial state in quantum and classical processes

We consider the additional entropy production (EP) incurred by a fixed quantum or classical process on some initial state $ρ$, above the minimum EP incurred by the same process on any initial state. We show that this additional EP, which we term the "mismatch cost of $ρ$", has a universal information-theoretic form: it is given by the contraction of the relative entropy between $ρ$ and the least-dissipative initial state $φ$ over time. We derive versions of this result for integrated EP incurred over the course of a process, for trajectory-level fluctuating EP, and for instantaneous EP rate. We also show that mismatch cost for fluctuating EP obeys an integral fluctuation theorem. Our results demonstrate a fundamental relationship between "thermodynamic irreversibility" (generation of EP) and "logical irreversibility" (inability to know the initial state corresponding to a given final state). We use this relationship to derive quantitative bounds on the thermodynamics of quantum error correction and to propose a thermodynamically-operationalized measure of the logical irreversibility of a quantum channel. Our results hold for both finite and infinite dimensional systems, and generalize beyond EP to many other thermodynamic costs, including nonadiabatic EP, free energy loss, and entropy gain.

quant-ph↗

arXiv2022

A Novel Approach to the Partial Information Decomposition

We consider the "partial information decomposition" (PID) problem, which aims to decompose the information that a set of source random variables provide about a target random variable into separate redundant, synergistic, union, and unique components. In the first part of this paper, we propose a general framework for constructing a multivariate PID. Our framework is defined in terms of a formal analogy with intersection and union from set theory, along with an ordering relation which specifies when one information source is more informative than another. Our definitions are algebraically and axiomatically motivated, and can be generalized to domains beyond Shannon information theory (such as algorithmic information theory and quantum information theory). In the second part of this paper, we use our general framework to define a PID in terms of the well-known Blackwell order, which has a fundamental operational interpretation. We demonstrate our approach on numerous examples and show that it overcomes many drawbacks associated with previous proposals.

cs.IT↗

arXiv2021

Work, entropy production, and thermodynamics of information under protocol constraints

In many real-world situations, there are constraints on the ways in which a physical system can be manipulated. We investigate the entropy production (EP) and extractable work involved in bringing a system from some initial distribution $p$ to some final distribution $p'$, given that the set of master equations available to the driving protocol obeys some constraints. We first derive general bounds on EP and extractable work, as well as a decomposition of the nonequilibrium free energy into an "accessible free energy" (which can be extracted as work, given a set of constraints) and an "inaccessible free energy" (which must be dissipated as EP). In a similar vein, we consider the thermodynamics of information in the presence of constraints, and decompose the information acquired in a measurement into "accessible" and "inaccessible" components. This decomposition allows us to consider the thermodynamic efficiency of different measurements of the same system, given a set of constraints. We use our framework to analyze protocols subject to symmetry, modularity, and coarse-grained constraints, and consider various examples including the Szilard box, the 2D Ising model, and a multi-particle flashing ratchet.

cond-mat.stat-mech↗

arXiv2021

Entropy production given constraints on the energy functions

We consider the problem of driving a finite-state classical system from some initial distribution $p$ to some final distribution $p'$ with vanishing entropy production (EP), under the constraint that the driving protocols can only use some limited set of energy functions $\mathcal{E}$. Assuming no other constraints on the driving protocol, we derive a simple condition that guarantees that such a transformation can be carried out, which is stated in terms of the smallest probabilities in $\{p,p'\}$ and a graph-theoretic property defined in terms of $\mathcal{E}$. Our results imply that a surprisingly small amount of control over the energy function is sufficient (in particular, any transformation $p\to p'$ can be carried out as soon as one can control some one-dimensional parameter of the energy function, e.g., the energy of a single state). We also derive a lower bound on the EP under more general constraints on the transition rates, which is formulated in terms of a convex optimization problem.

cond-mat.stat-mech↗

arXiv2020

Greetings from a Triparental Planet

In this work of speculative science, scientists from a distant star system explain the emergence and consequences of triparentalism, when three individuals are required for sexual reproduction, which is the standard form of mating on their home world. The report details the evolution of their reproductive system--that is, the conditions under which triparentalism and three self-avoiding mating types emerged as advantageous strategies for sexual reproduction. It also provides an overview of the biological consequences of triparental reproduction with three mating types, including the genetic mechanisms of triparental reproduction, asymmetries between the three mating types, and infection dynamics arising from their different mode of sexual reproduction. The report finishes by discussing how central aspects of their society, such as short-lasting unions among individuals and the rise of a monoculture, might have arisen as a result of their triparental system.

q-bio.PE↗