اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدThermodynamics of duplication thresholds in synthetic protocell systems
104
0
0.0
(
0
)
تأليف
Bernat Corominas-Murtra
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract -- yet realistic -- synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural -- and eventually, functional -- elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around $sim 10^{-13}{rm J}$. Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.
قيم البحث
اقرأ أيضاً
Structure-forming systems are ubiquitous in nature, ranging from atoms building molecules to self-assembly of colloidal amphibolic particles. The understanding of the underlying thermodynamics of such systems remains an important problem. Here we der
ive the entropy for structure-forming systems that differs from Boltzmann-Gibbs entropy by a term that explicitly captures clustered states. For large systems and low concentrations, the approach is equivalent to the grand-canonical ensemble; for small systems, we find significant deviations. We derive the detailed fluctuation theorem and Crooks work fluctuation theorem for structure-forming systems. The connection to the theory of particle self-assembly is discussed. We apply the results to several physical systems. We present the phase diagram for patchy particles described by the Kern-Frenkel potential. We show that the Curie-Weiss model with molecule structures exhibits a first-order phase transition.
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop a compact
-- i.e. relying on a reduced set of parameters -- thermodynamic model of metabolism, in order to analyze the chemical-to-mechanical energy conversion under muscle load, and give a thermodynamic ground to Hills seminal muscular operational response model. Living organisms are viewed as dynamical systems experiencing a feedback loop in the sense that they can be considered as thermodynamic systems subjected to mixed boundary conditions, coupling both potentials and fluxes. Starting from a rigorous derivation of generalized thermoelastic and transport coefficients, leading to the definition of a metabolic figure of merit, we establish the expression of the chemical-mechanical coupling, and specify the nature of the dissipative mechanism and the so called figure of merit. The particular nature of the boundary conditions of such a system reveals the presence of a feedback resistance, representing an active parameter, which is crucial for the proper interpretation of the muscle response under effort in the framework of Hills model. We also develop an exergy analysis of the so-called maximum power principle, here understood as a particular configuration of an out-of-equilibrium system, with no supplemental extremal principle involved.
The paper by Malek Mansour and Garcia [Phys. Rev. E 101, 052135 (2020)] is shown to be based on misconceptions in the stochastic formulation of chemical thermodynamics in reactive systems. Their erroneous claims, asserting that entropy production can
not be correctly evaluated using path probabilities whenever the reactive system involves more than one elementary reaction leading to the same composition changes, are refuted.
The nature of the behaviour of an isolated many-body quantum system periodically driven in time has been an open question since the beginning of quantum mechanics. After an initial transient, such a system is known to synchronize with the driving; in
contrast to the non-driven case, no fundamental principle has been proposed for constructing the resulting non-equilibrium state. Here, we analytically show that, for a class of integrable systems, the relevant ensemble is constructed by maximizing an appropriately defined entropy subject to constraints, which we explicitly identify. This result constitutes a generalisation of the concepts of equilibrium statistical mechanics to a class of far-from-equilibrium-systems, up to now mainly accessible using ad-hoc methods.
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and this process
is referred to as `translation of the genetic message encoded in the sequence of mRNA transcript. In each successful chemo-mechanical cycle during the (protein) elongation stage, the ribosome elongates the protein by a single subunit, called amino acid, and steps forward on the template mRNA by three nucleotides called a codon. Therefore, a ribosome is also regarded as a molecular motor for which the mRNA serves as the track, its step size is that of a codon and two molecules of GTP and one molecule of ATP hydrolyzed in that cycle serve as its fuel. What adds further complexity is the existence of competing pathways leading to distinct cycles, branched pathways in each cycle and futile consumption of fuel that leads neither to elongation of the nascent protein nor forward stepping of the ribosome on its track. We investigate a model formulated in terms of the network of discrete chemo-mechanical states of a ribosome during the elongation stage of translation. The model is analyzed using a combination of stochastic thermodynamic and kinetic analysis based on a graph-theoretic approach. We derive the exact solution of the corresponding master equations. We represent the steady state in terms of the cycles of the underlying network and discuss the energy transduction processes. We identify the various possible modes of operation of a ribosome in terms of its average velocity and mean rate of GTP hydrolysis. We also compute entropy production as functions of the rates of the interstate transitions and the thermodynamic cost for accuracy of the translation process.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
