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J. Ricardo Arias-Gonzalez

Publications and source records attributed to J. Ricardo Arias-Gonzalez.

8 recordsLinked to original sources
arXiv2026

Sense-Making phase transition framework for Affect

Contemporary accounts of affect emphasize different perspectives, ranging from the regulation of bodily states in allostatic approaches to the relational and sense-making character stressed by enactive theories. Here, we show that affect can be made explicit within the sense-making phase transition framework previously introduced for the perception of an inner sensation. Within this same formal structure, each stable minimum of the sense-making potential defines an affective state: its position determines valence, while its depth determines arousal. Affect therefore is not introduced as an independent ingredient, but emerges as the associated state in the valence-arousal space, providing a link between allostatic and enactive approaches to affect. This formulation distinguishes valence intensity from arousal, allows for dominant and secondary affective states, and naturally accommodates mixed-valence configurations beyond a strictly bipolar description. Revisiting representative landscapes of the model, we show how neutral, uncertain, polarized, and mixed-valence regimes arise as a function of contextual sensory information, learned historical evaluation, and externally supplied information. We further show that the resulting valence-arousal relation provides a theoretical basis for the upper-open V-shaped organization discussed in the affect literature, while also opening a natural route toward a dynamical description of affect and emotions.

q-bio.NC↗
arXiv2026

Spin-Based Modeling of Perception as Emergent from contextualized Internal Evaluation

We develop a microscopic model of perception of an interoceptive sensation in which spin-like variables encode an organism's internal evaluation of embodied vital norms associated with the sensation. Spins can take positive, negative, or neutral values. These local valorizations interact on a lattice embedded in the environmental context, and their collective configuration gives rise to a macroscopic perceptual state. By applying a coarse-graining procedure to a family of symmetric spin models, we derive a macroscopic Landau-type functional that makes explicit the mechanism by which key phenomenological features of perception, emerge from microscopic evaluative interactions. A central result is that the inclusion of a neutral evaluative state fundamentally alters the structure of the perceptual landscape, enhancing entropy, lowering the critical threshold, and increasing sensitivity to contextual input. These results establish a principled link between microscopic evaluative processes and large-scale perceptual organization, offering a flexible framework for integrating perceptual regulation and neurobiological modeling. The model integrates notions of neuroscience and cognitive science using the formalism of condensed matter field theory and providing novel theoretical insights and experimental predictions for conditions such as mental disorders and chronic pain.

q-bio.NC↗
arXiv2023

Multiplexed vortex beam-based optical tweezers

The design and implementation of a multiplexed spiral phase mask in an experimental optical tweezer setup are presented. This diffractive optical element allows the generation of multiple concentric vortex beams with independent topological charges. The generalization of the phase mask for multiple concentric vortices is also shown. The design for a phase mask of two multiplexed vortices with different topological charges is developed. We experimentally show the transfer of angular momentum to the optically trapped microparticles by enabling orbiting dynamics around the optical axis independently within each vortex. The angular velocity of the confined particles versus the optical power in the focal region is also discussed for different combinations of topological charges.

physics.optics↗
arXiv2016

A general framework for microscopically reversible processes with memory

Statistical Mechanics deals with ensembles of microstates that are compatible with fixed constraints and that on average define a thermodynamic macrostate. The evolution of a small system is normally subjected to changing constraints and involve a stochastic dependence on previous events. Here, we develop a theory for reversible processes with memory that comprises equilibrium statistics and that converges to the same physics in the limit of independent events. This framework is based on the characterization of single phase-space pathways and is used to derive ensemble-average dynamics in stochastic systems driven by a protocol in the limit of no friction. We show that the state of a system depends on its history to the extent of attaining a one-to-one correspondence between states and pathways when memory covers all the previous events. Equilibrium appears as the consequence of exploring all pathways that connect two states by all procedures. This theory is useful to interpret single-molecule experiments in Biophysics and other fields in Nanoscience and an adequate platform for a general theory of irreversible processes.

cond-mat.stat-mech↗
arXiv2015

A general theory for irreversible thermodynamics

We demonstrate that irreversibility arises from the principle of microscopic reversibility and the presence of memory in the time evolution of a single copy of a system driven by a protocol. We introduce microscopic reversibility by using the concept of protocol- and pathway-dependent thermodynamic function, as defined in J.R. Arias-Gonzalez, arXiv:1511.08017 [cond-mat.stat-mech], and memory by using the concept of non-Markovianity, as in J.R. Arias-Gonzalez, arXiv:1511.06139 [cond-mat.stat-mech]. We define work as the change in free energy and heat as the change in entropy for micoscopic, individual pathways of a system subject to a protocol. We find that all non-equilibrium statistics emerge naturally. In particular, we derive most known fluctuation theorems and formulate two others. While the conservation of energy is invoked both at the level of the individual pathway and in ensemble-average processes, the second law of thermodynamics and the time arrow, which are only fulfilled in ensemble-average processes, are shown to be consequences of microscopic reversibility and non-Markovianity.

cond-mat.stat-mech↗
arXiv2015

Statistical physics of directional, stochastic chains with memory

Stochastic chains represent a wide and key variety of phenomena in many branches of science within the context of Information Theory and Thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Here, we demonstrate that when memory is introduced, the statistics of the system depends on the mechanism by which objects or symbols are assembled, even in the slow dynamics limit wherein friction can be neglected. To analyse these systems, we introduce a sequence-dependent partition function, investigate its properties and compare it to the standard normalization defined by the statistical physics of ensembles. Then, we study the behaviour of the entropy and the internal energy in this intrinsic, directional chains finding that they vary around their thermally-induced equilibrium analogues due to memory effects. We anticipate that our results are necessary to interpret configurational order and information transfer in many molecular systems within Materials Science, Biophysics, Communication and Engineering.

cond-mat.stat-mech↗
arXiv2012

Entropy involved in fidelity of DNA replication

Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorporation of the nucleotides. The copied strand is, to first order of approximation, a state of independent and non-indentically distributed random variables for which the nucleotide that is incorporated by the polymerase at each step is dictated by the template strand, and to second order of approximation, a state of non-uniformly distributed random variables with nearest-neighbor interactions for which the recognition of secondary structure by the polymerase in the resultant double-stranded polymer determines the entropy of the replicated strand. Two incorporation mechanisms arise naturally and their biological meanings are explained. It is known that replication occurs far from equilibrium and therefore the Shannon entropy here derived represents an upper bound for replication to take place. Likewise, this entropy sets a universal lower bound for the copying fidelity in replication.

physics.bio-ph↗