Sisir Roy

National Institute of Advanced Studies

This is an editorial piece for a special issue (SI) in Frontiers of Psychology on 'The Varieties of Contemplative Experiences and Practices'. While diverse contemplative techniques are employed across a plethora of traditions around the world, contemplative research over the years has not reflected this variety. Despite exponential growth in contem...

2 Stromal cells possess unique properties to regenerate themselves and cure various chronic 3 illnesses. An easily available and ethical source for procurement of stromal cells is umbilical cord 4 blood which is now being stored for future use. Vedic texts also describe the cord blood as a 5 source of life. However, Indian traditions seem to preser...

What is cognition? Equivalently, what is cognition good for? Or, what is it that would not be but for human cognition? But for human cognition, there would not be science. Based on this kinship between individual cognition and collective science, here we put forward Isbell conjugacy-the adjointness between objective geometry and subjective algebra-...

Decision making from thermodynamics perspective

Stromal cells possess unique properties to regenerate themselves and cure various chronic illnesses. An easily available and ethical source for procurement of stromal cells is umbilical cord blood which is now being stored for future use. Vedic texts also describe the cord blood as a source of life. However, Indian traditions seem to preserve one m...

Thermodynamics studies the relations between heat, work, temperature, and energy. The laws of thermodynamics describe how the energy in a system changes and whether the system can perform useful work on its surroundings. Thermodynamics has proved fruitful in many fields, such as chemistry, biology, and economics, and gives us hope for cognitive ana...

Twenty-four astronomers and physicists from ten countries have signed a petition protesting the censorship of papers that are critical of the Big Bang Hypothesis by the open pre-print website arXiv.

Recent observational evidence in extra galactic astronomy, the interpretation of the nature of quasar redshift continues to be research interest. Spectrum observation of high redshift quasar is young in nature. Observational evidence discuss on physical interpretation of redshift periodicity with statistical confirmation. Karlsson observed redshift...

Cell-to-cell communication processes in the bacterial world can be considered as a collective bacterial behavior, which is coordinated by chemical signaling molecules (autoinducers, quorum sensing molecules, or pheromones). This complex biological process is termed the quorum sensing mechanism, which is considered a density-dependent bacterial comm...

Cell-to-cell communication processes in the bacterial world can be considered as a collective bacterial behavior, which is coordinated by chemical signaling molecules (autoinducers, quorum sensing molecules, or pheromones). This complex biological process is termed the quorum sensing mechanism, which is considered a density-dependent bacterial comm...

The recent progress of scientific researches on the neuronal correlates of various types of meditation practices raise debates and challenges to modern neuroscience. The characterization of various states of meditation as described in Hindu as well as in Buddhist traditions is a fascinating area of research. Noise as unwanted variation in meditatio...

This book illustrates the role of randomness and noise in living organisms. Traditionally, the randomness and noise have been used in understanding signal processing in communications. This book is divided into two sections, the first of which introduces readers to the various types and sources of noise and the constructive role of noise in non-lin...

Stochastic fluctuation is an inevitable property of life at cellular and molecular level. Noise plays a pivotal role in genetic networks and synthetic genetic networks. Amplitude of noise is regulated by the transcription rate, regulatory dynamics and genetic factors. We explore the concept of stochastic fluctuations at molecular level. Moreover, w...

Concept of noise and randomness is discussed in science and technology for many decades. Generally, noise plays a destructive role in science and technology, whereas it plays a constructive role in case of living organisms. Various types of noise as well as their representations are discussed in this chapter. Difference between classical and quantu...

Noise is an inevitable part of any physical and biological system. It is considered an unwanted evil from the point of view of physical systems. We emphasize various types of noise and their sources, which include thermal noise, short noise, excess noise, low frequency noise and quantum noise.

Noise plays a significant role in the living systems. The functional role of stochastic fluctuations varies from time to time. Various types of noise change the dynamics of the biological phenomena. Here, we explore the concept of noise in cellular level (i.e. cellular noise) and focus on gene expression noise. We quantify intrinsic and extrinsic n...

The concept of randomness and determinism is discussed in both eastern and western philosophies for many centuries. The developments of physical science as well as biological science raise new debates about the role of randomness and determinism. The epistemic and ontic nature of randomness is discussed in this chapter. The issues related to the la...

Cellular communication is the fundamental process of sharing information by using signalling molecules. We design and construct a synthetic gene regulatory network in a bacterial cell and study the effect of intracellular and extracellular noise in the cell–cell communication system.

Nonlinear dynamics is widely used in the context of physical, chemical, engineering and biological sciences. In this chapter, we present the basic theory of nonlinear dynamics with examples. Here, we mainly discuss the introductory concept of dynamical systems that include the linear systems, non-local theory of nonlinear systems, global theory of...

In case of living organisms, the term ‘noise’ usually refers to the variance amongst measurements obtained from repeated identical experimental conditions, or from output signals from these systems. It is noteworthy that both these conditions are universally characterized by the presence of background fluctuations. In non-living systems, such as el...

The concept of chaos plays an important role in nonlinear systems—both in physical systems and in living organisms. Chaoschaos occurs in deterministic systems. The word stochasticitystochasticity is synonymous with the word randomness, whereas in deterministic system no random or noise component is there in the describing equation. However, the con...

Development is a very complex and robust process. In this chapter, we have discussed the concept of developmental noise as well as the mechanism of developmental stability at different levels, which include organismal, developmental system and molecular level.

Gene oscillatorsoscillators are fascinating field of research where fundamental properties of life are studied by the combination of experimental and theoretical views. NoiseNoise is considered as an inherent part of these systems. In this chapter, we discuss several complex oscillating biological processes that include circadian rhythms,circadian...

Noise influences synchronization process of oscillatory networks. It helps us to understand the dynamics of the collective oscillatory networks as well as the conditions for synchronization. In this chapter, we address the two uncoupled mathematical models such as Pikovsky–Rabinovich circuit model and Hindmarsh–Rose neuron model to study synchroniz...

Ion channel plays a very important role in information processing of brain. The opening and closing of gate of the channel is a random process characterized by Markovian one. The noise associated with this random process may also affect the cognitive domain. The role of channel noise in Hodgkin–Huxley equation and co-operativity of neurons is discu...

In the present scenario of the world, where there is a sharp decline of moral and ethical values across the globe making individual and social structures appear chaotic, cultivating prosociality seems to be crucial while we deal with different people, groups and organizations. While the study of prosocial behaviours is usually dealt in the areas of...

This book introduces the concept of bacterial communication systems from a mathematical modeling point of view. It sheds light on the research undertaken in the last three decades, and the mathematical models that have been proposed to understand the underlying mechanism of such systems. These communication systems are related to quorum sensing mec...

Cell communication process mediates the swarming motility (phenotype) of the bacterial community. Swarming phenomena is triggered by the threshold level of chemical signal and secreted factors. This chapter deals with the mathematical framework of the swarming behaviour, which is regulated by quorum sensing. We emphasise on the agent base mathemati...

Cell-cell conversation mechanism controls bacterial virulence factors which are considered as sources for different bacterial infection diseases. These pathogenic bacteria are widespread in living systems. Here, we discuss significant mathematical formalism (i.e. deterministic and stochastic model) for the process of endosome escape via virulence f...

The bacterial quorum sensing mechanism regulates the gene expression. Autoinducers play a key role to control the system. We emphazise the effective distance range of quorumsensing process, spatiotemporal patterns of gene expression and Turing patterns in gene circuit in this chapter.

Bacteria are communicated using small diffusible chemical signalling molecules. This communication process controls other bacterial social behaviours such as cooperation, conflict and cheating. In this chapter, we model the bacterial diverse and fascinating social lives. The mathematical formalism of evolutionary models deal with bacterial social a...

In this chapter, we are accumulating significant experimental results of the quorum sensing mechanism over the last few decades. We summarise important experimental observations of several talking bacteria such as Vibrio fischeri,Pseudomomonas aeruginosa, Agrobacterium tumefaciens, Erwinia carotovora, Vibrio harveyi, Vibrio anguillarum, Yersinia en...

Synthetic biology is an interdisciplinary subject where we are taking about the rewiring, re-engineering and design principal of the living systems for understanding the undiscovered underlying mechanism of complex biological systems. Here, we discuss mainly synthetic biological approaches related to bacterial communication systems which includes g...

Besides bacterial quorum sensing mechanism, bacterial communicate also through electrical signalling mechanism. This electrical communication process is mediated by potassium ion-channels. Here, we explore the reconciliation in bacterial biofilms, metabolic codependence model with extended version, potassium ion channel based electrical communicati...

Bacterial communication systems are very interactive which controls several biological functions. Noise is an inherent property of biological communication systems. This chapter deals with the effect of noise in the bacterial communication mechanism with the help of weakly non-local hydrodynamics and viscosity. The theoretical framework is based on...

We consider noise as an inevitable part of living and non-living systems.We know synthetic biology is an interdisciplinary field. Engineering and basic science are patched up to understand complex biological phenomena. We discuss in details about the conception of noise in synthetic biology form destructive point of view and/or engineer point of vi...

Noise is usually thought as an unwanted signal in the study of science and technology. The introduction of stochastic resonance in nonlinear dynamical systems change our view of the role of noise (in living systems) from the destructive nature to constructive one. We highlight some recent time observations on the role of noise in synthetic systems....

Bacteria are unicellular microorganism, which can communicate through three different ways such as chemical signalling mechanisms, acoustic wave process and electrical signalling mechanism for their survival in distinct environmental conditions. Chemical signalling process is formally known as quorum sensing, which is extensively studied by many mi...

Bacterial quorum sensing mechanism is considered as the gene expression regulator in response to fluctuations in bacterial cell-population density. This communication process is controlled by autoinducers. So bacteria can talk to each other using autoinducers. We introduce bacterial talking mechanism or communication process in this chapter. We bri...

Bacterial biofilm is considered as a complex biological phenomenon. The development of the bacterial biofilms are regulated by quorum sensing mechanism. Biofilms have a significant importance in medical science because it is directly related to life threatening diseases. This chapter deals with the mathematical models of biofilms formation which in...

Bacterial cell communication process is modelled mathematically with emphasis on the molecular mechanism of the gram negative and gram positive bacterium. This chapter mainly focus on the mathematical formalism of the lux regulatory model, up-down regulatory model, Dockery-Keener model, complex formation model and the dynamical model of Staphylococ...

Noise plays an important role in science, engineering as well as in biological systems. The destructive role of noise has been extensively discussed in communication systems. The discovery of the phenomena called stochastic resonance clearly indicates the constructive role of noise for the nonlinear systems and hence in case of biological systems....

Noise play an important role in science, engineering aswell as in biological systems. The destructive role of noise has been extensively discussed in communication systems. The discovery of the phenomena called stochastic resonance clearly indicates the constructive role of noise for the non-linear systems and hence in case of biological systems. H...

Bacterial communication systems regulate virulence factors and play a key role in different bacterial infection diseases. In this chapter, we address the concept of quorum quenching and discuss mathematical models of anti-quorum sensing which are useful for the treatment purpose. Models predictions are significant for the future experimentations.

Bacterial cell communication process is modelled mathematically with emphasis on the molecular mechanism of the gram-negative and gram-positive bacteria. This chapter mainly focuses on the mathematical formalism of the lux regulatory model, up-down regulatory model, Dockery-Keener model, complex formation model and the dynamical model of Staphyloco...

The present article is limited to research studies focused on understanding the phenomenon and construction of the concept of ‘Self.’ When we look at one’s experience of the Self, as a whole, it involves various components associated with different aspects like self-identification, self-location and the sense of the existence of oneself or the sens...

Owing to its benefits on various cognitive aspects, one’s emotions and wellbeing, meditation has drawn interest from several researchers and common public alike. We have different meditation practices associated with many cultures and traditions across the globe. Current literature suggests significant changes in the neural activity among the diffe...

Studying the mechanisms and pathways of waste clearance in the brain received much attention lately because of their functional significance and clinical implications (1,2). In a recent study (3), Hablitz et al., made an attempt to bring us one step closer in tackling the puzzling question of how and when the brain clears its waste. Here, the autho...

In modern physics, the properties like charge, spin, etc. of elementary entities like electron, proton, photon, etc. are considered to be “intrinsic properties” of the entity. Intrinsic properties are those properties that a thing possesses, irrespective of whether or not there are other contingent things. In Buddhist philosophy especially in Mādhy...

The recent findings clearly indicate that bacteria communicate with each other as well as with the surrounding. This communication is done through chemical molecules as well through electrical signaling. Moreover, the bacteria organize and make various structures in Biofilm. We call these types of behaviors of bacteria as intelligence.

There exists no individual who does not exhibit prosociality in one or the other situation of their lifetime. But the argument is, to what extent? Whether it arises spontaneously out of true empathy and compassion for others or it is goal-oriented with some hidden motive? Here, our primary intention is to convey that, though various meditation-base...

Meditation and yoga have become so popular that we not only started devising new interventions based on these practices in the context of health and wellbeing, but in the process, we also deviated from the actual purpose and goals set by different traditions. Numerous scientific studies have been conducted on different practices of meditation to st...

In recent years, a surge of interest came up with studies in terms of the influence of different types of meditation on the brain and body. Lacking the basic understanding as to why ancient cultures conceived this practice primarily in its various facets, most of these studies mainly focus on delineating the underlying mechanisms of influence in te...

Notions such as Sunyata, Catuskoti, and Indra’s Net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nagarjuna considered two levels of reality: one called conventional reality and the other ultimate reality. Within this framework, Sun...

It is found in the recent experiments that the viscosity of water increases when the inner lining of nano-cavity is hydrophilic as well as hydrophobic. However, the viscosity increases dramatically in case of hydrophilic surface. In recent works [1,2] the present author along with his collaborators visualized this kind of situation within K-ion cha...

We showed that quantum mechanical superposition can sustain in the process of ion transfer in protein membrane for a substantial period in spite of the presence of the interactions with environmental modes of molecular vibration. The spectral temperature, as defined in quantum thermodynamical framework plays a significant role in maintaining the co...

Owing to its benefits on various cognitive aspects, emotions and one’s wellbeing meditation have drawn much interest from several researchers and common public alike. We have different meditation practices associated with numerous cultures and traditions across the globe. In addition, current literature also suggests distinct differences in neural...

There exists no individual who doesn’t exhibit prosociality in one or the other situation of their lifetime. But the argument is, to what extent, and whether it arises spontaneously out of true empathy and compassion for others or goal-oriented with some hidden motive? Here, our primary intention is to convey that, though various meditation-based i...

The term soul is used in the traditional literature as a synonym for one’s true Self and is associated with the subjective essence of one’s living. Since, we don’t have any means to quantify it, the science has ruled out this idea from its investigations. But, in a recent study, Ceylan et al. (2017) has reintroduced the word soul to scientific lite...

The recent findings confirm that bacteria communicate each other through chemical and electrical signals. Bacteria use chemical signaling molecules, which are called as quorum sensing molecules (QSMs) or autoinducers. Moreover, the ion channels in bacteria conduct a long-range electrical signaling within biofilm communities through propagated waves...

In Bærentsen (2015), various issues have been raised mainly concerning the contemporary view of the practice of meditation with respect to the actual philosophical perspective. We endorse the idea of referring to ancient traditional sources on meditation - as a practice and thus are in agreement with the many of the points discussed in Bærentsen (2...

Cognition involves physical stimulation, neural coding, mental conception, and conscious perception. Beyond the neural coding of physical stimuli, it is not clear how exactly these component processes constitute cognition. Within mathematical sciences, category theory provides tools such as category, functor, and adjoint-ness, which are indispensab...

Our failure in devising effective clinical measures for different sleep disorders results from the fact that we don't really understand the role and functioning of sleep in maintaining the body to its extent. Within this context, we share a possible connection between meditation and sleep and discuss how the study of one may help in understanding t...

Bacteria are unicellular microorganism, which are found in nature quite often. They talk to each other using chemical signaling process (quorum sensing) and ion-channel mediated electrical signaling mechanism. Quorum sensing is a density dependent bacterial collective behaviour and/or cell-to -cell communication mechanism. This widespread bacterial...

Scientists and philosophers start questioning the existence of free will using the new discoveries in physical science as well as in neuroscience. The impression that we are able to freely choose between different possible courses of action is fundamental to our mental life but it is also suggested that this subjective experience is not more than a...

Notions such as Sunyata, Catuskoti, and Indra’s Net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nagarjuna considered two levels of reality: one called conventional reality and the other ultimate reality. Within this framework, Sun...

Clinical neuroscience has becoming a very useful discipline mainly because of the spectacular technological developments like electroencephalogram(EEG), Functional Magnetic Resonance(FMRI), Positron Emission Tomography(PET), Transcra-nial Magnetic Stimulation(TMS), Diffusion Tensor Imaging(DTI), Magneto-encephalography(MEG) etc. With the help of th...

Do the methods and models to support the decision-making process guarantee the quality of the results? The search for satisfactory answers to this question has aroused interest in users, scientists and engineers who develop the theory and applications oriented, above all, the industrial sector. Cognitive processes, during their development, need to...

We perform new experiment using almost the same sample size considered by Tversky and Shafir to test the validity of classical probability theory in decision making. The results clearly indicate that the disjunction effect depends also on culture and more specifically on gender (females rather than males). We did more statistical analysis rather th...

It has long been recognized that certain bacterial groups exhibit cooperative behavioral patterns. Bacteria accomplish such communication via exchange of extracellular signaling molecules called pheromones(autoinducer or quorum sensing molecules). As the bacterial culture grows, signal molecules are released into extracellular milieu accumulate, ch...

To understand the concept of quantum probability and its application to the cognitive domain, it is necessary to explain the basic concepts of quantum theory. Again, to understand the basic concepts of quantum theory one needs to understand the formalism of Hilbert space. There are several postulates in understanding quantum theory. These postulate...

The complementary principle was introduced by Niels Bohr to explain the mutually exclusive aspects of quantum entities like electron, photon etc. Since Bohr’s elaboration, it has been extensively discussed in many branches of science. This principle states that two aspects of a quantum entity, such as wave and particle aspects, cannot be measured s...

Recent experimental findings clearly suggest that classical probability theory is still not successful to explain modalities in human cognition, especially in connection to decision making. The major problem seems to be the presence of epistemic uncertainty and its effects on cognition at any time point. Moreover, the stochasticity in the model ari...

In general, two paradigms deal with the categorization of decision theories: the descriptive and normative theories. Descriptive theories are based on empirical observations and on experimental studies of choice behaviors. But the normative theories specifically assume a rational decision-maker who follows well-defined preferences of behaviors as w...

Recently, series of experiments have been performed with human subjects where the law of addition of probabilities in classical probability theory has been shown to be invalid within the context of decision making in the cognitive domain. These results are classified into six different categories. The concept of quantum probability has been introdu...

Since the very inception of quantum theory, the corresponding logic for quantum entities has attracted much attention. The logic underlying the quantum theory is shown to be non-Boolean in character. Boolean logic is a two/valued logic which is used for the description of everyday objects. Modern computers are based on this logic. The existence of...

The decision making from a neuroscience perspective is one of the outstanding problems in twenty first-century science. The evolution of higher brain function has given us the capacity for flexible decision making. Gerstner et al. (Neuronal Dynamics: From Single Neurons to Networks and Models of Cognition. Cambridge University Press, Cambridge, 201...

The central issue in brain function is to understand how the internalization of the properties of the external world is realized within an internal functional space. By the term “internalization” of the properties, we mean the ability of the nervous system to fracture external reality into sets of sensory messages; the next task of this process is...

Recent advances in understanding quantum reality lead to the proposal of quantum ontology. Here, as such, there is no distinction between the classical and the non-classical world. This is based on the abstract framework of propositional calculus which gives rise to Hilbert space structure, in which case, the framework is devoid of any material con...

We showed that quantum mechanical superposition can sustain in the process of ion transfer in protein membrane for a substantial period in spite of the presence of the interactions with environmental modes of molecular vibration. The spectral temperature, as defined in quantum thermodynamical framework plays a significant role in maintaining the co...

Norbert Wiener and Claude Shannon introduced information theory independently in 1948. Shannon introduced it to quantify the amount of data that can be transmitted by communication devices. It causes considerable confusion when it was applied to biological system. This theory deals with the capacity of the system to transmit information, not with t...

Water fluidity is modified, in a nontrivial manner, by the presence of bacteria above a threshold number density. Under such threshold conditions swimming bacterial suspensions impose a coordinated water movement on a length scale of the order (10–100) micrometers compared with a bacterial size of the order of 3 micrometers. This observation leads...

In this paper, we have estimated the temperature dependent path predictability for an electronic Mach-Zehnder interferometer. The increment of path predictability can directly be associated with stronger decoherence process. We have also theoretically predicted that placing two detectors in both the paths, which are at the same equilibrium temperat...

ABSTRACT Quantum entanglement is a property of a quantum state consisting of two or more microscopic objects like photons, electrons, neutrons etc. The objects producing the joint state i.e., entangled state is not separable but makes a non-local connection between the objects separated by arbitrary distance. The concept of non-locality is a metaph...

This book discusses the paradigm of quantum ontology as an appropriate model for measuring cognitive processes. It clearly shows the inadequacy of the application of classical probability theory in modelling the human cognitive domain. The chapters investigate the context dependence and neuronal basis of cognition in a coherent manner. According to...

The purpose of the decision-making process is to determine the results while committing a categorical statement or proposition. A statement or proposition is a sentence which is either true or false. A categorical proposition or statement relates two classes or categories. This process is used widely in many disciplines, for example, in complex sci...

Water fluidity is modified, in a nontrivial manner, by the presence of bacteria above a threshold number density. Under such threshold conditions swimming bacterial suspensions impose a coordinated water movement on a length scale of the order (10-100) micrometers compared with a bacterial size of the order of 3 micrometers. This observation leads...

In our recent book (Abraham and Roy, 2010) we have proposed a mathematical model for the quantum vacuum as a model of consciousness. We emphasized that the quantum vacuum is not identical to cosmic consciousness. The word akasha is translated in English as space or ether. In the Eastern tradition ether has two phases, subtle and gross. In our model...