Glassy Dynamics of Protein Folding

A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis dynamics at low temperatures with the exponent $\beta\simeq 1/4$, in agreement with the best experimental results. The time dependent correlation functions for fluctuations about the native state, computed in the Gaussian approximation for real proteins, have also been found to have the same functional form. Our results indicate that the energy landscape exhibits universal features over a very large range of energies and is relatively independent of the specific dynamics.Comment: RevTeX, 4 pages, multicolumn, including 5 figures; larger computations performed, error bars improve

Strategies for the evolution of sex

We find that the hypothesis made by Jan, Stauffer and Moseley [Theory in Biosc., 119, 166 (2000)] for the evolution of sex, namely a strategy devised to escape extinction due to too many deleterious mutations, is sufficient but not necessary for the successful evolution of a steady state population of sexual individuals within a finite population. Simply allowing for a finite probability for conversion to sex in each generation also gives rise to a stable sexual population, in the presence of an upper limit on the number of deleterious mutations per individual. For large values of this probability, we find a phase transition to an intermittent, multi-stable regime. On the other hand, in the limit of extremely slow drive, another transition takes place to a different steady state distribution, with fewer deleterious mutations within the asexual population.Comment: RevTeX, 11 pages, multicolumn, including 12 figure

Dissipative dynamics and the statistics of energy states of a Hookean model for protein folding

A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean spring connecting pails or hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process and giving rise Lo the so-called Wigner distribution. A tunably fine- or coarse-grained sampling of the energy landscape yields a family of distributions for the energies and energy spacings.Publisher's Versio

The statistics of energy states of a Hookean model for proteins

A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobia residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process with reflecting boundary conditions, and giving rise to distributions of the Wigner or inverse Gaussian form. A continuum approximation leads to a path integral formulation of the problem.Publisher's Versio

The statistics of energy states of a Hookean model for proteins

A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process with reflecting boundary conditions, and giving rise to distributions of the Wigner or inverse Gaussian form. A continuum approximation leads to a path integral formulation of the problem. PACS 5.65+b,5.70Ln,87.17.AaA generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process with reflecting boundary conditions, and giving rise to distributions of the Wigner or inverse Gaussian form. A continuum approximation leads to a path integral formulation of the problem. PACS 5.65+b,5.70Ln,87.17.A

Türkiye'de Orta ve Büyük Ölçekli Mantar İşletmelerinin Değerlendirilmesi

The commercial production of cultivated-mushroom, which has a forty years of past in Turkey, was started after 1980s. Until the recent decade, most of the total amount of production in Turkey was performed by family members while the cultivation of the product has gained an upward trend since the beginning of 2000s, though the amount and development rate were not enough. During that time, a number of large (;gt;2000 m2 ) and medium (500-2000 m2 ) scale mushroom production facilities were established and Turkey has gained an important place in mushroom production in the world. In this study, we aimed to reveal the common production methods of ten medium and large scale mushroom companies whose daily production capacities are above 1 ton in six regions. In this respect, all companies have been visited and communicated directly with company representatives and a survey comprising 65 questions about company, production facility, compost and casing soil, production systems, diseases and pests and packaging was made. The findings have suggested us that such companies have mostly a history of 15 years of time and have a land size of 10-50 thousand m2 , while their mushroom production areas vary between in size and that they make use of technology in production and automation in their plants and they have quality management systems (ITU, ISO 9001, ISO 22000 and Global Gap ) and they employ generally qualified and experienced technicians or agriculture engineers and also that 40% of them receive consultancy and also that they use their own productions or standard ready mycelium planted compost and that they use domestic peat as casing material and that they package the mushrooms with their brands and sell to markets mostly and lastly that they conduct pre-sale quality sorting and grading. It was also seen that there is lack of food engineers employed and most of the companies do not receive consultancy, and that the waste compost is not evaluated correctly and that the covering material is not in the required standards and that there are even companies not doing any water analysis and that coal for heating and chemicals for disinfection are used and that diseases and pests are inevitable and last that they lack in processing different products.Ülkemizde 40 yıllık bir geçmişe sahip olan kültür mantarı yetiştiriciliğinde ticari üretime 1980'li yıllardan sonra başlanmıştır. Son 10 yıla kadar ülkemizde toplam mantar üretim miktarının büyük bir çoğunluğu küçük aile işletmelerinden elde edilmekteyken, 2000'li yılların başından itibaren üretim miktarı ve gelişim hızı yeterli olmamakla birlikte yetiştiricilik hızlı bir yükselişe geçmiştir. Bu süre içerisinde ülkemizin farklı bölgelerinde orta (500-2000 m2) ve büyük ölçekli (>2000 m2) birçok mantar üretim tesisi kurulmuş ve ülkemiz dünya kültür mantarı üretiminde önemli bir yere sahip olmuştur. Yürütülen bu çalışmada, ülkemizde kültür mantarı yetiştiriciliğinin yoğun olarak yapıldığı 6 bölgemizde, günlük üretim kapasitesi 1 ton ve üzeri olan toplam 10 orta ve büyük ölçekli mantar işletmesinin genel üretim sistemlerinin ortaya konulması amaçlanmıştır. Bu amaçla 2015 yılında tüm firmalar ziyaret edilerek, firma yetkilileri ile doğrudan görüşülmüş; firma, üretim tesisi, kompost ve örtü toprağı, üretim sistemleri, hastalık ve zararlı, paketleme, kalite-yönetim sistemleri hakkında 65 sorudan oluşan bir anket yapılmıştır. Elde edilen sonuçlar bu tür firmaların çoğunun 15 yıllık bir geçmişe sahip olduğunu, arazi büyüklüklerinin 10-50 bin m2, mantar üretim alanlarının 5-10 bin m2 arasında değiştiğini, üretimde teknolojiyi ve işletmelerinde otomasyonu kullandıklarını, kalite yönetim sistemlerine (ITU, ISO 22000 vs) sahip olduklarını, işletmelerinde genellikle mantarcılık konusunda deneyimli tekniker ve ziraat mühendisi bulundurduklarını, %40'ının danışmandan yararlandığını, üretimde kendi üretimi veya dışarıdan misel ekilmiş hazır standart kompost kullandıklarını, örtü materyali olarak yerli torf kullandıklarını, üretilen mantarları markaları ile paketlediklerini ve genellikle marketlere sattıklarını, satış öncesinde kalite tasniflemesi ve boylama yaptıklarını belirtmişlerdir. İşletmelerde gıda mühendisi sayısının azlığı, hepsinin danışmandan yararlanmadığı, atık kompostun doğru değerlendirilmediği, örtü materyalinin istenilen kriterlerde olmadığı, hiç su analizi yaptırmayan firmanın var olduğu, ısıtmada kömür, dezenfeksiyonda kimyasal maddelerin kullanıldığı, hastalık ve zararlıların kaçınılmaz olduğu, farklı ürün işleme sistemlerinin yetersiz olduğu görülmüştü

Evaluation of Medium and Large-Scale Mushroom Companies in Turkey

Ülkemizde 40 yıllık bir geçmişe sahip olan kültür mantarı yetiştiriciliğinde ticari üretime 1980'li yıllardan sonra başlanmıştır. Son 10 yıla kadar ülkemizde toplam mantar üretim miktarının büyük bir çoğunluğu küçük aile işletmelerinden elde edilmekteyken, 2000'li yılların başından itibaren üretim miktarı ve gelişim hızı yeterli olmamakla birlikte yetiştiricilik hızlı bir yükselişe geçmiştir. Bu süre içerisinde ülkemizin farklı bölgelerinde orta (500-2000 m2) ve büyük ölçekli (>2000 m2) birçok mantar üretim tesisi kurulmuş ve ülkemiz dünya kültür mantarı üretiminde önemli bir yere sahip olmuştur. Yürütülen bu çalışmada, ülkemizde kültür mantarı yetiştiriciliğinin yoğun olarak yapıldığı 6 bölgemizde, günlük üretim kapasitesi 1 ton ve üzeri olan toplam 10 orta ve büyük ölçekli mantar işletmesinin genel üretim sistemlerinin ortaya konulması amaçlanmıştır. Bu amaçla 2015 yılında tüm firmalar ziyaret edilerek, firma yetkilileri ile doğrudan görüşülmüş; firma, üretim tesisi, kompost ve örtü toprağı, üretim sistemleri, hastalık ve zararlı, paketleme, kalite-yönetim sistemleri hakkında 65 sorudan oluşan bir anket yapılmıştır. Elde edilen sonuçlar bu tür firmaların çoğunun 15 yıllık bir geçmişe sahip olduğunu, arazi büyüklüklerinin 10-50 bin m2, mantar üretim alanlarının 5-10 bin m2 arasında değiştiğini, üretimde teknolojiyi ve işletmelerinde otomasyonu kullandıklarını, kalite yönetim sistemlerine (ITU, ISO 22000 vs) sahip olduklarını, işletmelerinde genellikle mantarcılık konusunda deneyimli tekniker ve ziraat mühendisi bulundurduklarını, %40'ının danışmandan yararlandığını, üretimde kendi üretimi veya dışarıdan misel ekilmiş hazır standart kompost kullandıklarını, örtü materyali olarak yerli torf kullandıklarını, üretilen mantarları markaları ile paketlediklerini ve genellikle marketlere sattıklarını, satış öncesinde kalite tasniflemesi ve boylama yaptıklarını belirtmişlerdir. İşletmelerde gıda mühendisi sayısının azlığı, hepsinin danışmandan yararlanmadığı, atık kompostun doğru değerlendirilmediği, örtü materyalinin istenilen kriterlerde olmadığı, hiç su analizi yaptırmayan firmanın var olduğu, ısıtmada kömür, dezenfeksiyonda kimyasal maddelerin kullanıldığı, hastalık ve zararlıların kaçınılmaz olduğu, farklı ürün işleme sistemlerinin yetersiz olduğu görülmüştürThe commercial production of cultivated-mushroom, which has a forty years of past in Turkey, was started after 1980s. Until the recent decade, most of the total amount of production in Turkey was performed by family members while the cultivation of the product has gained an upward trend since the beginning of 2000s, though the amount and development rate were not enough. During that time, a number of large (>2000 m2 ) and medium (500-2000 m2 ) scale mushroom production facilities were established and Turkey has gained an important place in mushroom production in the world. In this study, we aimed to reveal the common production methods of ten medium and large scale mushroom companies whose daily production capacities are above 1 ton in six regions. In this respect, all companies have been visited and communicated directly with company representatives and a survey comprising 65 questions about company, production facility, compost and casing soil, production systems, diseases and pests and packaging was made. The findings have suggested us that such companies have mostly a history of 15 years of time and have a land size of 10-50 thousand m2 , while their mushroom production areas vary between in size and that they make use of technology in production and automation in their plants and they have quality management systems (ITU, ISO 9001, ISO 22000 and Global Gap ) and they employ generally qualified and experienced technicians or agriculture engineers and also that 40% of them receive consultancy and also that they use their own productions or standard ready mycelium planted compost and that they use domestic peat as casing material and that they package the mushrooms with their brands and sell to markets mostly and lastly that they conduct pre-sale quality sorting and grading. It was also seen that there is lack of food engineers employed and most of the companies do not receive consultancy, and that the waste compost is not evaluated correctly and that the covering material is not in the required standards and that there are even companies not doing any water analysis and that coal for heating and chemicals for disinfection are used and that diseases and pests are inevitable and last that they lack in processing different products