arXiv subjects

Michal Kolář

Publications and source records attributed to Michal Kolář.

16 recordsLinked to original sources

arXiv2026

Reverse translocation of a nascent polypeptide through the ribosomal exit tunnels

Before they mature, all known proteins translocate through the ribosomal exit tunnel in a form of extended or partially folded nascent polypeptide. This translocation occurs in the natural direction from the peptidyl transferase centre buried deep in the large ribosomal subunit through a tunnel to the ribosomal surface. Some proteins, however, enter the ribosomal tunnel from outside and translocate in the reverse direction. In this work, we address a simple question: to what extent is the ribosomal tunnel intrinsically directional. To compare the forward and reverse peptide translocations, we performed biased molecular dynamics simulations and assessed the directionality of tunnels from four different organisms using a model poly-alanine decapeptide. Our simulations reveal that the tunnel architecture intrinsically favours the natural direction translocation from peptidyl transferase centre to the ribosomal surface. Consequently, proteins that occupy the tunnel in the reverse direction likely require dedicated structural machinery to overcome this intrinsic bias.

physics.bio-ph↗

arXiv2025

Local quantum coherence with intersource interactions at nonzero temperature

Local quantum coherence in a two-level system (TLS) is typically generated via time-dependent driving. However, it can also emerge autonomously from symmetry-breaking interactions between the TLS and its surrounding environment at a low temperature. Although such environments often consist of interacting atoms or spins, the role of interactions within the environment in generating the autonomous local coherence has remained unexplored. Here, we address this gap by analyzing an exactly solvable model, which comprises a target TLS coupled to $N$ interacting source TLSs that represent the environment, with the whole system being in thermal equilibrium. We show that the local coherence not only persists but can be enhanced at finite temperatures of the environment compared to the case of no inter-source interactions. The temperature dependence of the coherence bears signatures of a quantum phase transition, and our analytical results suggest strategies for its optimization. Our findings reveal generic properties of the autonomously generated quantum coherence and point to viable routes for observing the coherence at nonzero temperatures.

quant-ph↗

arXiv2024

Negative Wigner function by decaying interaction from equilibrium

Bosonic systems with negative Wigner function superposition states are fundamentally witnessing nonlinear quantum dynamics beyond linearized systems and, recently, have become essential resources of quantum technology with many applications. Typically, they appear due to sophisticated combination of external drives, nonlinear control, measurements or strong nonlinear dissipation of subsystems to an environment. Here, we propose a conceptually different and more autonomous way to obtain such states, avoiding these ingredients, using purely sudden interaction decay in the paradigmatic interacting qubit-oscillator system weakly coupled to bath at thermal equilibrium in a low-temperature limit. We demonstrate simultaneously detectable unconditional negative Wigner function and quantum coherence and their qualitative enhancement employing more qubits.

quant-ph↗

arXiv2023

Local coherence by thermalized intra-system coupling

Quantum superposition of energy eigenstates can appear autonomously in a single quantum two-level system coupled to a low-temperature thermal bath, if such coupling has a proper composite nature. We propose here a principally different and more feasible approach employing engineered interactions between two-level systems being thermalized into a global Gibbs state by weakly coupled thermal bath at temperature $T$. Therefore, in such case quantum coherence appears by a different mechanism, whereas the system-bath coupling does not have to be engineered. We demonstrate such autonomous coherence generation reaching maximum values of coherence. Moreover, it can be alternatively built up by using weaker but collective interaction with several two-level systems. This approach surpasses the coherence generated by the engineered system-bath coupling for comparable interaction strengths and directly reduces phase estimation error in quantum sensing. This represents a necessary step towards the autonomous quantum sensing.

quant-ph↗

arXiv2022

Measurement Induced Synthesis of Coherent Quantum Batteries

Quantum coherence represented by a superposition of energy eigenstates is, together with energy, an important resource for quantum technology and thermodynamics. Energy and quantum coherence however, can be complementary. The increase of energy can reduce quantum coherence and vice versa. Recently, it was realized that steady-state quantum coherence could be autonomously harnessed from a cold environment. We propose a conditional synthesis of $N$ independent two-level systems (TLS) with partial quantum coherence obtained from an environment to one coherent system using a measurement able to increase both energy and coherence simultaneously. The measurement process acts here as a Maxwell demon synthesizing the coherent energy of individual TLS to one large coherent quantum battery. The measurement process described by POVM elements is diagonal in energy representation and, therefore, it does not project on states with quantum coherence at all. We discuss various strategies and their efficiency to reach large coherent energy of the battery. After numerical optimization and proof-of-principle tests, it opens way to feasible repeat-until-success synthesis of coherent quantum batteries from steady-state autonomous coherence.

quant-ph↗

arXiv2022

Pairwise Measurement Induced Synthesis of Quantum Coherence

Quantum coherent superpositions of states with different energies, i.e., states with coherence with respect to energy basis, are important resource for modern quantum technologies. States with small coherence can be obtained either autonomously, due to the effect of a weak coherent drive or, potentially, due to the presence of an environment. In this paper, we propose a measurement-based protocol for quantum coherence synthesis from individual systems (with low initial coherence) into a global (and higher) coherence of the joint system. As an input, it uses $N$ non-interacting copies of two-level systems (TLS), with low initial energy and coherence. These can be supplied by, e.g., a weak external drive or can result from an interaction with a bath. This protocol conditionally synthesizes an output state with higher energy and coherence than the initial state had, representing an universal process whose rules have not been well studied, yet. In addition to energy and coherence, we study the quantity called mutual coherence, showing increase after the protocol application, as well. This approach is based on application of sequential pairwise projective measurements on TLS pairs (conditionally removing their ground states), that are diagonal in the TLS energy basis. The functionality of the coherence synthesis is robust with respect to dephasing effects of the TLS environment on the system. Our approach may show its benefits in quantum sensing, quantum batteries charging, or other applications where synthesis of a larger coherent system from smaller (weaker) resources is useful.

quant-ph↗

arXiv2022

Enhanced steady-state coherence via repeated system-bath interactions

The appearance of steady-state coherence (SSC) from system-bath interaction proves that quantum effects can appear without an external drive. Such SSC could become a resource to demonstrate quantum advantage in the applications. We predict the generation of SSC if the target system repeatedly interacts with independent and non-correlated bath elements. To describe their behavior, we use the collision model approach of system-bath interaction, where the system interacts with one bath element (initially in an incoherent state) at a time, asymptotically (in the fast-collision regime) mimicking a macroscopic Markovian bath coupled to the target system. Therefore, the SSC qualitatively appears to be the same as if the continuous Markovian bath would be used. We confirm that the presence of composite system-bath interactions under the rotating-wave approximation (RWA) is the necessary condition for the generation of SSC using thermal resources in collision models. Remarkably, we show that SSC substantially increases if the target system interacts collectively with more than one bath element at a time. Already few bath elements collectively interacting with the target system are sufficient to increase SSC at non-zero temperatures at the cost of tolerable lowering the final state purity. From the thermodynamic perspective, the SSC generation in our collision models is inevitably linked to a non zero power input (and thus heat dissipated to the bath) necessary to reach the steady-state, although such energetic cost can be lower compared to cases relying on SSC non generating interactions.

quant-ph↗

arXiv2021

Experimental demonstration of optimal probabilistic enhancement of quantum coherence

We theoretically and experimentally investigate conditional enhancement of overall coherence of quantum states by probabilistic quantum operations that apply to the input state a quantum filter diagonal in the basis of incoherent states. We identify the optimal filters that for a given probability of successful filtering maximize the output coherence. We verify the performance of the studied quantum filters in a proof-of-principle experiment with linear optics, where a pair of two-level quantum systems is represented by polarization states of two photons. We comprehensively characterize the implemented two-qubit linear optical quantum filters by full quantum process tomography and we experimentally observe the optimal quantum coherence enhancement by quantum filtering.

quant-ph↗

arXiv2019

Heat capacities of thermally manipulated mechanical oscillator at strong coupling

Coherent quantum oscillators are basic physical systems both in quantum statistical physics and quantum thermodynamics. Their realizations in lab often involve solid-state devices sensitive to changes in ambient temperature. We represent states of the solid-state optomechanical oscillator with temperature-dependent frequency by equivalent states of the mechanical oscillator with temperature-dependent energy levels. We interpret the temperature dependence as a consequence of strong coupling between the oscillator and the heat bath. We explore parameter regimes corresponding to anomalous behavior of mechanical and thermodynamic characteristics as a consequence of the strong coupling: (i) The localization and the purification induced by heating, and (ii) the negativity of two generalized heat capacities. The capacities can be used to witness non-linearity in the temperature dependency of the energy levels. Our phenomenological experimentally-oriented approach can stimulate development of new optomechanical and thermomechanical experiments exploring basic concepts of strong coupling thermodynamics.

quant-ph↗

arXiv2017

Optomechanical oscillator controlled by variation in its heat bath temperature

We propose a generation of a low-noise state of optomechanical oscillator by a temperature dependent force. We analyze the situation in which a quantum optomechanical oscillator (denoted as the membrane) is driven by an external force (produced by the piston). Both systems are embedded in a common heat bath at certain temperature $T$. The driving force the piston exerts on the membrane is bath temperature dependent. Initially, for $T=T_0$, the piston is linearly coupled to the membrane. The bath temperature is then reversibly changed to $T\neq T_0$. The change of temperature shifts the membrane, but simultaneously also increases its fluctuations. The resulting equilibrium state of the membrane is analyzed from the point of view of mechanical, as well as of thermodynamic characteristics. We compare these characteristics of membrane and derive their intimate connection. Next, we cool down the thermal noise of the membrane, bringing it out of equilibrium, still being in the contact with heat bath. This cooling retains the effective canonical Gibbs state with the effective temperature $T^\star$. In such case we study the analogs of the equilibrium quantities for low-noise mechanical states of the membrane.

quant-ph↗

arXiv2015

Criticality and Spin Squeezing in the Rotational Dynamics of a BEC on a Ring Lattice

We examine the dynamics of circulating modes of a Bose-Einstein condensate confined in toroidal lattice. Nonlinearity due to interactions leads to criticality that separates oscillatory and self-trapped phases among counter-propagating modes which however share the same physical space. In the mean-field limit, the criticality is found to substantially enhance sensitivity to rotation of the system. Analysis of the quantum dynamics reveals the fluctuations near criticality are significant, that we explain using spin-squeezing formalism visualized on a Bloch sphere. We utilize the squeezing to propose a Ramsey interferometric scheme that suppresses fluctuation in the relevant quadrature sensitive to rotation.

cond-mat.quant-gas↗

arXiv2015

Spin squeezing by tensor twisting and Lipkin-Meshkov-Glick dynamics in a toroidal Bose-Einstein condensate with spatially modulated nonlinearity

We propose a scheme for spin-squeezing in the orbital motion of a Bose-Einstein condensate (BEC) in a toroidal trap. A circular lattice couples two counter-rotating modes and squeezing is generated by the nonlinear interaction spatially modulated at half the lattice period. By varying the amplitude and phase of the modulation, various cases of the twisting tensor can be directly realized, leading to different squeezing regimes. These include one-axis twisting and the two-axis counter-twisting which are often discussed as the most important paradigms for spin squeezing. Our scheme naturally realizes the Lipkin-Meshkov-Glick model with the freedom to vary all its parameters simultaneously.

cond-mat.quant-gas↗

arXiv2012

Quantum bath refrigeration towards absolute zero: unattainability principle challenged

A minimal model of a quantum refrigerator (QR), i.e. a periodically phase-flipped two-level system permanently coupled to a finite-capacity bath (cold bath) and an infinite heat dump (hot bath), is introduced and used to investigate the cooling of the cold bath towards the absolute zero (T=0). Remarkably, the temperature scaling of the cold-bath cooling rate reveals that it does not vanish as T->0 for certain realistic quantized baths, e.g. phonons in strongly disordered media (fractons) or quantized spin-waves in ferromagnets (magnons). This result challenges Nernst's third-law formulation known as the unattainability principle.

quant-ph↗

arXiv2007

From Protein Interactions to Functional Annotation: Graph Alignment in Herpes

Sequence alignment forms the basis of many methods for functional annotation by phylogenetic comparison, but becomes unreliable in the `twilight' regions of high sequence divergence and short gene length. Here we perform a cross-species comparison of two herpesviruses, VZV and KSHV, with a hybrid method called graph alignment. The method is based jointly on the similarity of protein interaction networks and on sequence similarity. In our alignment, we find open reading frames for which interaction similarity concurs with a low level of sequence similarity, thus confirming the evolutionary relationship. In addition, we find high levels of interaction similarity between open reading frames without any detectable sequence similarity. The functional predictions derived from this alignment are consistent with genomic position and gene expression data.

q-bio.MN↗

arXiv2004

Minimizing energy below the glass thresholds

Focusing on the optimization version of the random K-satisfiability problem, the MAX-K-SAT problem, we study the performance of the finite energy version of the Survey Propagation (SP) algorithm. We show that a simple (linear time) backtrack decimation strategy is sufficient to reach configurations well below the lower bound for the dynamic threshold energy and very close to the analytic prediction for the optimal ground states. A comparative numerical study on one of the most efficient local search procedures is also given.

cond-mat.dis-nn↗

arXiv2003

Selective advantage of topological disorder in biological evolution

We examine a model of biological evolution of Eigen's quasispecies in a holey fitness landscape, where the fitness of a site is either 0 (lethal site) or a uniform positive constant (viable site). So, the evolution dynamics is determined by the topology of the genome space. It is modeled by the random Bethe lattice. We use the effective medium and single-defect approximations to find the criteria, under which the localized quasispecies cloud is created. We find that shorter genomes, which are more robust to random mutations than average, represent a selective advantage which we call ``topological''. A way of assessing empirically the relative importance of reproductive success and topological advantage is suggested.

cond-mat.stat-mech↗